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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB OF HIV-1 GP120 V3-SPECIFIC HUMAN MONOCLONAL ANTIBODY 2424 IN COMPLEX WITH JR-FL V3 PEPTIDE
 
Authors :  X. -P. Kong, R. Pan
Date :  14 Jan 15  (Deposition) - 08 Jul 15  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.18
Chains :  Asym. Unit :  H,I,J,L,M,N,P,Q,R
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  I,M,Q  (1x)
Biol. Unit 3:  J,N,R  (1x)
Keywords :  Hiv-1 Gp120, Monoclonal Antibody, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kumar, R. Pan, C. Upadhyay, L. Mayr, S. Cohen, X. H. Wang, P. Balasubramanian, A. Nadas, M. S. Seaman, S. Zolla-Pazner, M. K. Gorny, X. P. Kong, C. E. Hioe
Functional And Structural Characterization Of Human V3-Specific Monoclonal Antibody 2424 With Neutralizing Activity Against Hiv-1 Jrfl.
J. Virol. V. 89 9090 2015
PubMed-ID: 26109728  |  Reference-DOI: 10.1128/JVI.01280-15

(-) Compounds

Molecule 1 - LIGHT CHAIN OF HIV-1 GP120 V3-SPECIFIC HUMAN MONOCLONAL ANTIBODY 2424
    Chains: L, M, N
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HEAVY CHAIN OF HIV-1 GP120 V3-SPECIFIC HUMAN MONOCLONAL ANTIBODY 2424
    Chains: H, I, J
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HIV-1 JR-FL GP120 V3 PEPTIDE
    Chains: P, Q, R
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : HIJLMNPQR
Biological Unit 1 (1x): H  L  P  
Biological Unit 2 (1x):  I  M  Q 
Biological Unit 3 (1x):   J  N  R

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4XMK)

(-) Sites  (0, 0)

(no "Site" information available for 4XMK)

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3I:22 -I:92
4I:140 -I:196
5J:22 -J:92
6J:140 -J:196
7L:23 -L:88
8L:133 -L:193
9M:23 -M:88
10M:133 -M:193
11N:23 -N:88
12N:133 -N:193

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:139 -Pro L:140
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Ser M:7 -Pro M:8
6Tyr M:139 -Pro M:140
7Phe I:146 -Pro I:147
8Glu I:148 -Pro I:149
9Ser N:7 -Pro N:8
10Tyr N:139 -Pro N:140
11Phe J:146 -Pro J:147
12Glu J:148 -Pro J:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XMK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XMK)

(-) Exons   (0, 0)

(no "Exon" information available for 4XMK)

(-) 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 H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.eee.....eeeeeeee.......eeeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeeee......eeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xmk H    1 EVQLVGSGGGLIQPGGSLRLSCAASDFSVSEYYMTWVRQAPGKGLEWVAVLYKDGSQFYAPSVKGRFIVSRDNSKNSLYLQMNNLRGEDTAVYFCARENADYGSDYYFGMDVWGQGTAVAVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSSVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEP  213
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G       110       120      |136       146       156       166       176       186       196       206       
                                                                                                            82A||               100A||||||                        127|                                                                               
                                                                                                             82B|                100B|||||                         134                                                                               
                                                                                                              82C                 100C||||                                                                                                           
                                                                                                                                   100D|||                                                                                                           
                                                                                                                                    100E||                                                                                                           
                                                                                                                                     100F|                                                                                                           
                                                                                                                                      100G                                                                                                           


Chain I from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeeee......eeeeeee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xmk I    1 EVQLVGSGGGLIQPGGSLRLSCAASDFSVSEYYMTWVRQAPGKGLEWVAVLYKDGSQFYAPSVKGRFIVSRDNSKNSLYLQMNNLRGEDTAVYFCARENADYGSDYYFGMDVWGQGTAVAVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSSVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEP  213
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G       110       120      |136       146       156       166       176       186       196       206       
                                                                                                            82A||               100A||||||                        127|                                                                               
                                                                                                             82B|                100B|||||                         134                                                                               
                                                                                                              82C                 100C||||                                                                                                           
                                                                                                                                   100D|||                                                                                                           
                                                                                                                                    100E||                                                                                                           
                                                                                                                                     100F|                                                                                                           
                                                                                                                                      100G                                                                                                           


Chain J from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.eee.....eeeeeeee.......eeeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeeee......eeeeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4xmk J    1 EVQLVGSGGGLIQPGGSLRLSCAASDFSVSEYYMTWVRQAPGKGLEWVAVLYKDGSQFYAPSVKGRFIVSRDNSKNSLYLQMNNLRGEDTAVYFCARENADYGSDYYFGMDVWGQGTAVAVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSSVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEP  213
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G       110       120     ||137       147       157       167       177       187       197       207      
                                                                                                            82A||               100A||||||                       126|                                                                               
                                                                                                             82B|                100B|||||                        134                                                                               
                                                                                                              82C                 100C||||                                                                                                          
                                                                                                                                   100D|||                                                                                                          
                                                                                                                                    100E||                                                                                                          
                                                                                                                                     100F|                                                                                                          
                                                                                                                                      100G                                                                                                          


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee...ee..eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xmk L    1 DIVMNQSPPSLAVTPGEPASISCRASQSLLYSDGHNYLDWYLQKPGQAPQLLIYLGSTRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQPLQSYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  210
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     
                                                     27A||||                                                                                                                                                                                       
                                                      27B|||                                                                                                                                                                                       
                                                       27C||                                                                                                                                                                                       
                                                        27D|                                                                                                                                                                                       
                                                         27E                                                                                                                                                                                       


Chain M from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee...ee..eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xmk M    1 DIVMNQSPPSLAVTPGEPASISCRASQSLLYSDGHNYLDWYLQKPGQAPQLLIYLGSTRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQPLQSYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  210
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     
                                                     27A||||                                                                                                                                                                                       
                                                      27B|||                                                                                                                                                                                       
                                                       27C||                                                                                                                                                                                       
                                                        27D|                                                                                                                                                                                       
                                                         27E                                                                                                                                                                                       


Chain N from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee....ee...ee..eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xmk N    2 IVMNQSPPSLAVTPGEPASISCRASQSLLYSDGHNYLDWYLQKPGQAPQLLIYLGSTRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQPLQSYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFN  209
                                    11        21      |27D|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
                                                    27A||||                                                                                                                                                                                      
                                                     27B|||                                                                                                                                                                                      
                                                      27C||                                                                                                                                                                                      
                                                       27D|                                                                                                                                                                                      
                                                        27E                                                                                                                                                                                      


Chain P from PDB  Type:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .....hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                4xmk P  307 IHIGPGRAFYT  319
                              ||   318 
                            309|       
                             312       


Chain Q from PDB  Type:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .....hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                4xmk Q  307 IHIGPGRAFYT  319
                              ||   318 
                            309|       
                             312       


Chain R from PDB  Type:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .....hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                4xmk R  307 IHIGPGRAFYT  319
                              ||   318 
                            309|       
                             312
   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 4XMK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XMK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XMK)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Glu I:148 - Pro I:149   [ RasMol ]  
    Glu J:148 - Pro J:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Phe I:146 - Pro I:147   [ RasMol ]  
    Phe J:146 - Pro J:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Ser M:7 - Pro M:8   [ RasMol ]  
    Ser N:7 - Pro N:8   [ RasMol ]  
    Tyr L:139 - Pro L:140   [ RasMol ]  
    Tyr M:139 - Pro M:140   [ RasMol ]  
    Tyr N:139 - Pro N:140   [ RasMol ]  
 
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 Related Entries

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UniProtKB/Swiss-Prot
        ENV_HV1MN | P05877: 1acy 1ai1 1f58 1ggi 1k5m 1nak 1niz 1nj0 1q1j 2b0s 2qsc 3e6h 3go1 3mlw 3mlx 3uji 4m1d 4xaw 4xbe 4xc1 4xc3 4xcf

(-) Related Entries Specified in the PDB File

4xmk