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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYO-EM MODEL OF B41 SOSIP.664 IN COMPLEX WITH FRAGMENT ANTIGEN BINDING VARIABLE DOMAIN OF B12
 
Authors :  G. Ozorowski, J. Pallesen, A. B. Ward, C. A. Cottrell
Date :  28 Apr 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Keywords :  Neutralizing Antibody, Hiv-1, Envelope Glycoprotein, Receptor Binding Site, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Ozorowski, J. Pallesen, N. De Val, D. Lyumkis, C. A. Cottrell, J. L. Torres, J. Copps, R. L. Stanfield, A. Cupo, P. Pugach, J. P. Moore, I. A. Wilson, A. B. Ward
Open And Closed Structures Reveal Allostery And Pliability In The Hiv-1 Envelope Spike
Nature 2017
PubMed: search  |  Reference-DOI: 10.1038/NATURE23010

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
    Chains: G, D, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Gene: ENV
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - ENVELOPE GLYCOPROTEIN GP160
    Chains: A, B, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Gene: ENV
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 3 - B12 FAB HEAVY CHAIN
    Chains: H, F, I
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - B12 FAB LIGHT CHAIN
    Chains: L, J, K
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric/Biological Unit : ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 114)

Asymmetric/Biological Unit (3, 114)
No.NameCountTypeFull Name
1BMA12Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG99Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (0, 0)

(no "Site" information available for 5VN8)

(-) SS Bonds  (36, 36)

Asymmetric/Biological Unit
No.Residues
1A:598 -A:604
2B:598 -B:604
3C:598 -C:604
4D:54 -D:74
5D:126 -D:196
6D:131 -D:157
7D:218 -D:247
8D:228 -D:239
9D:296 -D:331
10D:378 -D:445
11D:385 -D:418
12D:501 -B:605
13E:54 -E:74
14E:126 -E:196
15E:131 -E:157
16E:218 -E:247
17E:228 -E:239
18E:296 -E:331
19E:378 -E:445
20E:385 -E:418
21E:501 -C:605
22F:22 -F:92
23G:54 -G:74
24G:126 -G:196
25G:131 -G:157
26G:218 -G:247
27G:228 -G:239
28G:296 -G:331
29G:378 -G:445
30G:385 -G:418
31G:501 -A:605
32H:22 -H:92
33I:22 -I:92
34J:23 -J:88
35K:23 -K:88
36L:23 -L:88

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Ser J:7 -Pro J:8
3Ser K:7 -Pro K:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VN8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VN8)

(-) Exons   (0, 0)

(no "Exon" information available for 5VN8)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 A  512 AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVHMLQLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQWEKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD  664
                                   521       531       541       565       575       585       595       605       615       625       635       645       655         
                                                               549|                                                                                                    
                                                                564                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 B  512 AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVHMLQLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQWEKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD  664
                                   521       531       541       565       575       585       595       605       615       625       635       645       655         
                                                               549|                                                                                                    
                                                                564                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 C  512 AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVHMLQLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQWEKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD  664
                                   521       531       541       565       575       585       595       605       615       625       635       645       655         
                                                               549|                                                                                                    
                                                                564                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eee........................eee.......ee.....hhhhhhh..hhhhhhh...............................................hhhhh................................eeeeee.......ee....eeee.............eee.........eee..........eeeeeeeeeeeeeeeeeee..........................eeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhhee.......eee.........................eeeeeee..ee.........ee.....eeeeeeeeeeeeeeee........eeeee......hhhhhh....eeeeee..eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 D   32 AKKWVTVYYGVPVWKEATTTLFCASDAATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQSLKTPLCVTLNCNNVNTMETGEMKNCSFNVTTSILFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQASFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV  505
                                    41        51      ||72        82        92       102       112    || 127       149       159     ||178      185D||||   191       201  ||   215       225       235       245       255       265       275       285       295       305   ||  317      |326       336       346       356  ||   367       377       387       398      |410       420       430       440       450       460       470       480       490       500     
                                                     58|                                            117|          136|             165|      185A|||||||                204|                                                                                                 309|        323A                                 359|                               395|     405|                                                                                                 
                                                      70                                             123           149              175       185B||||||                 209                                                                                                  312                                              361                                397      408                                                                                                 
                                                                                                                                               185C|||||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                185D||||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                 185E|||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                  185F||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                   185G|                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                    185H                                                                                                                                                                                                                                                                                                                       


Chain E from PDB  Type:PROTEIN  Length:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eee........................eee.......ee.....hhhhhhh..hhhhhhh...............................................hhhhh................................eeeeee.......ee....eeee.............eee.........eee..........eeeeeeeeeeeeeeeeeee..........................eeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhhee.......eee.........................eeeeeee..ee.........ee.....eeeeeeeeeeeeeeee........eeeee......hhhhhh....eeeeee..eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 E   32 AKKWVTVYYGVPVWKEATTTLFCASDAATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQSLKTPLCVTLNCNNVNTMETGEMKNCSFNVTTSILFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQASFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV  505
                                    41        51      ||72        82        92       102       112    || 127       149       159     ||178      185D||||   191       201  ||   215       225       235       245       255       265       275       285       295       305   ||  317      |326       336       346       356  ||   367       377       387       398      |410       420       430       440       450       460       470       480       490       500     
                                                     58|                                            117|          136|             165|      185A|||||||                204|                                                                                                 309|        323A                                 359|                               395|     405|                                                                                                 
                                                      70                                             123           149              175       185B||||||                 209                                                                                                  312                                              361                                397      408                                                                                                 
                                                                                                                                               185C|||||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                185D||||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                 185E|||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                  185F||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                   185G|                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                    185H                                                                                                                                                                                                                                                                                                                       


Chain F from PDB  Type:PROTEIN  Length:127
                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee......hhhhh.eeeeee.....eeeeeeee....eee.hhhhh..eeeeee....eeeeee...hhhhh.ee..ee......................ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 F    1 QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       
                                                                              52A                            82A||               100A|||||100J             
                                                                                                              82B|                100B|||||||              
                                                                                                               82C                 100C||||||              
                                                                                                                                    100D|||||              
                                                                                                                                     100E||||              
                                                                                                                                      100F|||              
                                                                                                                                       100G||              
                                                                                                                                        100H|              
                                                                                                                                         100I              


Chain G from PDB  Type:PROTEIN  Length:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eee........................eee.......ee.....hhhhhhh..hhhhhhh...............................................hhhhh................................eeeeee.......ee....eeee.............eee.........eee..........eeeeeeeeeeeeeeeeeee..........................eeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhhee.......eee.........................eeeeeee..ee.........ee.....eeeeeeeeeeeeeeee........eeeee......hhhhhh....eeeeee..eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 G   32 AKKWVTVYYGVPVWKEATTTLFCASDAATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQSLKTPLCVTLNCNNVNTMETGEMKNCSFNVTTSILFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQASFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV  505
                                    41        51      ||72        82        92       102       112    || 127       149       159     ||178      185D||||   191       201  ||   215       225       235       245       255       265       275       285       295       305   ||  317      |326       336       346       356  ||   367       377       387       398      |410       420       430       440       450       460       470       480       490       500     
                                                     58|                                            117|          136|             165|      185A|||||||                204|                                                                                                 309|        323A                                 359|                               395|     405|                                                                                                 
                                                      70                                             123           149              175       185B||||||                 209                                                                                                  312                                              361                                397      408                                                                                                 
                                                                                                                                               185C|||||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                185D||||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                 185E|||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                  185F||                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                   185G|                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                    185H                                                                                                                                                                                                                                                                                                                       


Chain H from PDB  Type:PROTEIN  Length:127
                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee......hhhhh.eeeeee.....eeeeeeee....eee.hhhhh..eeeeee....eeeeee...hhhhh.ee..ee......................ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 H    1 QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       
                                                                              52A                            82A||               100A|||||100J             
                                                                                                              82B|                100B|||||||              
                                                                                                               82C                 100C||||||              
                                                                                                                                    100D|||||              
                                                                                                                                     100E||||              
                                                                                                                                      100F|||              
                                                                                                                                       100G||              
                                                                                                                                        100H|              
                                                                                                                                         100I              


Chain I from PDB  Type:PROTEIN  Length:127
                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee......hhhhh.eeeeee.....eeeeeeee....eee.hhhhh..eeeeee....eeeeee...hhhhh.ee..ee......................ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vn8 I    1 QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       
                                                                              52A                            82A||               100A|||||100J             
                                                                                                              82B|                100B|||||||              
                                                                                                               82C                 100C||||||              
                                                                                                                                    100D|||||              
                                                                                                                                     100E||||              
                                                                                                                                      100F|||              
                                                                                                                                       100G||              
                                                                                                                                        100H|              
                                                                                                                                         100I              


Chain J from PDB  Type:PROTEIN  Length:108
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..............eeeee..........eeee.....eeeee.............eeee.....eeeee...hhhhh.ee...............ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                5vn8 J    1 EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGISDRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERK  107
                                    10        20       |29        39        49        59        69        79        89        99        
                                                     27A                                                                                


Chain K from PDB  Type:PROTEIN  Length:108
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..............eeeee..........eeee.....eeeee.............eeee.....eeeee...hhhhh.ee...............ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                5vn8 K    1 EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGISDRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERK  107
                                    10        20       |29        39        49        59        69        79        89        99        
                                                     27A                                                                                


Chain L from PDB  Type:PROTEIN  Length:108
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..............eeeee..........eeee.....eeeee.............eeee.....eeeee...hhhhh.ee...............ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                5vn8 L    1 EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGISDRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERK  107
                                    10        20       |29        39        49        59        69        79        89        99        
                                                     27A
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5VN8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VN8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VN8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5VN8)

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(no "Sites" information available for 5vn8)
 
  Cis Peptide Bonds
    Ser J:7 - Pro J:8   [ RasMol ]  
    Ser K:7 - Pro K:8   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
 

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 Databases and Analysis Tools

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Access by PDB/NDB ID
  5vn8
    Family and Domain Information: ProDom | SYSTERS
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  B3UES2_9HIV1 | B3UES2
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  B3UEZ6_9HIV1 | B3UEZ6
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        B3UES2_9HIV1 | B3UES2: 5vn3
        B3UEZ6_9HIV1 | B3UEZ6: 5vn3

(-) Related Entries Specified in the PDB File

5vn3