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(-) Description

Title :  STRUCTURE OF IMMATURE VRC01-CLASS ANTIBODY DRVIA7
 
Authors :  L. Kong, I. A. Wilson
Date :  02 Jul 15  (Deposition) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  G,H  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Vrc01, Hiv-1, Cd4 Binding Site, Gp120, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Kong, J. Bin, R. Li, Y. Chen, J. Liu, L. He, K. Hong, B. Su, Z. Wang, G. Ozorowski, X. Ji, Y. Hua, Y. Chen, M. C. Deller, Y. Hao, Y. Feng, F. Garces, R. Wilson, K. Dai, S. O'Dell, K. Mckee, M. Mascola, A. B. Ward R. T. Wyatt, Y. Li, I. A. Wilson, J. Zhu, Y. Shao
Critical Determinants In The Emergence Of Broadly Neutralizing Cd4-Binding Site Antibodies From An Hiv-1-Infected Chinese Donor
Immunity 2016
PubMed: search

(-) Compounds

Molecule 1 - DRVIA7 HEAVY CHAIN
    Chains: G, A, C, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DRVIA7 LIGHT CHAIN
    Chains: H, B, D, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x):       GH
Biological Unit 2 (1x): AB      
Biological Unit 3 (1x):   CD    
Biological Unit 4 (1x):     EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5CD3)

(-) Sites  (0, 0)

(no "Site" information available for 5CD3)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:139 -A:195
3B:23 -B:88
4B:136 -B:196
5C:22 -C:92
6C:139 -C:195
7D:23 -D:88
8D:136 -D:196
9E:22 -E:92
10E:139 -E:195
11F:23 -F:88
12F:136 -F:196
13G:22 -G:92
14G:139 -G:195
15H:23 -H:88
16H:136 -H:196

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Phe G:145 -Pro G:146
2Glu G:147 -Pro G:148
3Ser H:7 -Pro H:8
4Tyr H:142 -Pro H:143
5Phe A:145 -Pro A:146
6Glu A:147 -Pro A:148
7Ser B:7 -Pro B:8
8Tyr B:142 -Pro B:143
9Phe C:145 -Pro C:146
10Glu C:147 -Pro C:148
11Ser D:7 -Pro D:8
12Tyr D:142 -Pro D:143
13Phe E:145 -Pro E:146
14Glu E:147 -Pro E:148
15Ser F:7 -Pro F:8
16Tyr F:142 -Pro F:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CD3)

(-) Exons   (0, 0)

(no "Exon" information available for 5CD3)

(-) Sequences/Alignments

Asymmetric 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:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.hhhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........eee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd3 A    1 QVQLVESGTQFRRPGASVRLSCEASGYTFISSFIHWIRQGPGQGLEWMGWMNPRHGAVNYPRRFQGKVTMTRDTSIDTAYMELRDLRSDDTAMYFCVTSRTKDYDWDFVWGQGTLVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       132       142       152       162       172       182       192       202       212
                                                                              52A                            82A||               100A|||                                                                                                                
                                                                                                              82B|                100B||                                                                                                                
                                                                                                               82C                 100C|                                                                                                                
                                                                                                                                    100D                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd3 B    2 IQMTQSPVTLSASIGDRVTITCRASQRIDNWVAWYQQKPGRAPKLLIYKASILETGVPSRFSGSGSGTEFTLSINSLQPDDVATYYCQQFEEFGRGTKIDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  213
                                    11        21        31        41        51        61        71        81        91|      107       117       127       137       147       157       167       177       187       197       207      
                                                                                                                    91|    103|                                                                                                           
                                                                                                                     96     106                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee........eee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd3 C    1 QVQLVESGTQFRRPGASVRLSCEASGYTFISSFIHWIRQGPGQGLEWMGWMNPRHGAVNYPRRFQGKVTMTRDTSIDTAYMELRDLRSDDTAMYFCVTSRTKDYDWDFVWGQGTLVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       132       142       152       162       172       182       192       202       212
                                                                              52A                            82A||               100A|||                                                                                                                
                                                                                                              82B|                100B||                                                                                                                
                                                                                                               82C                 100C|                                                                                                                
                                                                                                                                    100D                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd3 D    2 IQMTQSPVTLSASIGDRVTITCRASQRIDNWVAWYQQKPGRAPKLLIYKASILETGVPSRFSGSGSGTEFTLSINSLQPDDVATYYCQQFEEFGRGTKIDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  213
                                    11        21        31        41        51        61        71        81        91|      107       117       127       137       147       157       167       177       187       197       207      
                                                                                                                    91|    103|                                                                                                           
                                                                                                                     96     106                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.hhhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........eee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd3 E    1 QVQLVESGTQFRRPGASVRLSCEASGYTFISSFIHWIRQGPGQGLEWMGWMNPRHGAVNYPRRFQGKVTMTRDTSIDTAYMELRDLRSDDTAMYFCVTSRTKDYDWDFVWGQGTLVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       132       142       152       162       172       182       192       202       212
                                                                              52A                            82A||               100A|||                                                                                                                
                                                                                                              82B|                100B||                                                                                                                
                                                                                                               82C                 100C|                                                                                                                
                                                                                                                                    100D                                                                                                                


Chain F from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd3 F    2 IQMTQSPVTLSASIGDRVTITCRASQRIDNWVAWYQQKPGRAPKLLIYKASILETGVPSRFSGSGSGTEFTLSINSLQPDDVATYYCQQFEEFGRGTKIDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  213
                                    11        21        31        41        51        61        71        81        91|      107       117       127       137       147       157       167       177       187       197       207      
                                                                                                                    91|    103|                                                                                                           
                                                                                                                     96     106                                                                                                           


Chain G from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee........eee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd3 G    1 QVQLVESGTQFRRPGASVRLSCEASGYTFISSFIHWIRQGPGQGLEWMGWMNPRHGAVNYPRRFQGKVTMTRDTSIDTAYMELRDLRSDDTAMYFCVTSRTKDYDWDFVWGQGTLVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       132       142       152       162       172       182       192       202       212
                                                                              52A                            82A||               100A|||                                                                                                                
                                                                                                              82B|                100B||                                                                                                                
                                                                                                               82C                 100C|                                                                                                                
                                                                                                                                    100D                                                                                                                


Chain H from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeee....eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd3 H    2 IQMTQSPVTLSASIGDRVTITCRASQRIDNWVAWYQQKPGRAPKLLIYKASILETGVPSRFSGSGSGTEFTLSINSLQPDDVATYYCQQFEEFGRGTKIDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  213
                                    11        21        31        41        51        61        71        81        91|      107       117       127       137       147       157       167       177       187       197       207      
                                                                                                                    91|    103|                                                                                                           
                                                                                                                     96     106
   Legend:   → Mismatch (orange background)
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    → 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 5CD3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CD3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CD3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5CD3)

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  Cis Peptide Bonds
    Glu A:147 - Pro A:148   [ RasMol ]  
    Glu C:147 - Pro C:148   [ RasMol ]  
    Glu E:147 - Pro E:148   [ RasMol ]  
    Glu G:147 - Pro G:148   [ RasMol ]  
    Phe A:145 - Pro A:146   [ RasMol ]  
    Phe C:145 - Pro C:146   [ RasMol ]  
    Phe E:145 - Pro E:146   [ RasMol ]  
    Phe G:145 - Pro G:146   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Ser D:7 - Pro D:8   [ RasMol ]  
    Ser F:7 - Pro F:8   [ RasMol ]  
    Ser H:7 - Pro H:8   [ RasMol ]  
    Tyr B:142 - Pro B:143   [ RasMol ]  
    Tyr D:142 - Pro D:143   [ RasMol ]  
    Tyr F:142 - Pro F:143   [ RasMol ]  
    Tyr H:142 - Pro H:143   [ RasMol ]  
 
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 Related Entries

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(-) Related Entries Specified in the PDB File

5cd5