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(-) Description

Title :  CRYSTAL STRUCTURE OF RABBIT MAB R20 FAB IN COMPLEX WITH V3 C-TERMINUS OF HIV-1 CONSENSUS B GP120
 
Authors :  R. M. Pan, X. P. Kong
Date :  16 Mar 13  (Deposition) - 31 Jul 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  H,I,L,M,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  I,M,Q  (1x)
Keywords :  Ig, Antibody, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Pan, J. M. Sampson, Y. Chen, M. Vaine, S. Wang, S. Lu, X. P. Kong
Rabbit Anti-Hiv-1 Monoclonal Antibodies Raised By Immunization Can Mimic The Antigen-Binding Modes Of Antibodies Derived From Hiv-1-Infected Humans.
J. Virol. V. 87 10221 2013
PubMed-ID: 23864637  |  Reference-DOI: 10.1128/JVI.00843-13

(-) Compounds

Molecule 1 - MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY R20 LIGHT CHAIN
    Chains: L, M
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: FAB
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 2 - MONOCLONAL ANTI-HIV-1 GP120 V3 ANTIBODY R20 HEAVY CHAIN
    Chains: H, I
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: FAB
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 3 - GP120
    Chains: P, Q
    Engineered: YES
    Fragment: THIRD VARIABLE REGION (V3) C-TERMINUS (UNP RESIDUES 48-62)
    Gene: ENV
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HILMPQ
Biological Unit 1 (1x): H L P 
Biological Unit 2 (1x):  I M Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER M:59 , ARG M:61 , GLN M:79BINDING SITE FOR RESIDUE SO4 M 301
2AC2SOFTWAREPRO M:8 , ALA M:9BINDING SITE FOR RESIDUE SO4 M 302

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:35A-H:50
3H:140 -H:193
4I:22 -I:92
5I:35A-I:50
6I:140 -I:193
7L:23 -L:88
8L:80 -L:170
9L:134 -L:193
10L:211 -H:127
11M:23 -M:88
12M:80 -M:170
13M:134 -M:193
14M:211 -I:127

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Thr L:7 -Pro L:8
2Phe L:140 -Pro L:141
3Leu H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Thr M:7 -Pro M:8
6Phe M:140 -Pro M:141
7Leu I:146 -Pro I:147
8Glu I:148 -Pro I:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JO3)

(-) Exons   (0, 0)

(no "Exon" information available for 4JO3)

(-) 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:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeeee......eeeeeee......eee.......eeeee....eeeeee...hhhhheeeeeeeeeeeeeee..eeeeeeeeeeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee......eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jo3 H    2 QSLEESGGDLVKPGASLTLTCTASGFSFTNNYYMCWVRQAPGKGLEWIACIYGGGRDIVFYATWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARENFDAVGVGGGTYSTDYYFDLWGPGTLVIVSSGQPKAPSVFPLAPCCGDTPSATVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAP  210
                                    11        21        31    |   40        50  ||    58        68        78    ||  86        96    ||100F|||||||103       113       123       133       143       153       163       173       183       193       203       
                                                            35A               52A|                            82A|               100A|||||100J|||                                                                                                              
                                                                               52B                             82B                100B|||||100K||                                                                                                              
                                                                                                                                   100C|||||100L|                                                                                                              
                                                                                                                                    100D|||||100M                                                                                                              
                                                                                                                                     100E||||                                                                                                                  
                                                                                                                                      100F|||                                                                                                                  
                                                                                                                                       100G||                                                                                                                  
                                                                                                                                        100H|                                                                                                                  
                                                                                                                                         100I                                                                                                                  


Chain I from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeeee......eeeeeee......eee.......eeeeeee..eeeeee...hhhhheeeeeeeeeeeeeee..eeeeeeeeeeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee......eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jo3 I    2 QSLEESGGDLVKPGASLTLTCTASGFSFTNNYYMCWVRQAPGKGLEWIACIYGGGRDIVFYATWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARENFDAVGVGGGTYSTDYYFDLWGPGTLVIVSSGQPKAPSVFPLAPCCGDTPSATVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAP  210
                                    11        21        31    |   40        50  ||    58        68        78    ||  86        96    ||100F|||||||103       113       123       133       143       153       163       173       183       193       203       
                                                            35A               52A|                            82A|               100A|||||100J|||                                                                                                              
                                                                               52B                             82B                100B|||||100K||                                                                                                              
                                                                                                                                   100C|||||100L|                                                                                                              
                                                                                                                                    100D|||||100M                                                                                                              
                                                                                                                                     100E||||                                                                                                                  
                                                                                                                                      100F|||                                                                                                                  
                                                                                                                                       100G||                                                                                                                  
                                                                                                                                        100H|                                                                                                                  
                                                                                                                                         100I                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4jo3l1 L:1-107 automated matches                                                                             d4jo3l2 L:108-211 automated matches                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..............eeeeee......eeeee..hhhhhhh.eeeeeeeeeee....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jo3 L    1 DIVMTQTPASVSAAVGGTVTINCQASETISNYLAWYQQKPGQPPKLLIYKASTLASGVSSRFKGSGSGTEYTLTISGVQCDDAATYYCQQGYSISDIDNSFGGGTEVVVKGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC  211
                                    10        20        30        40        50        60        70        80        90     |||97       107       117       127       137       147       157       167       177       187       197       207    
                                                                                                                         95A||                                                                                                                    
                                                                                                                          95B|                                                                                                                    
                                                                                                                           95C                                                                                                                    


Chain M from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4jo3m1 M:1-107 automated matches                                                                             d4jo3m2 M:108-211 automated matches                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee...eeeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee..............eeeeee......eeeee.....hhhh.eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jo3 M    1 DIVMTQTPASVSAAVGGTVTINCQASETISNYLAWYQQKPGQPPKLLIYKASTLASGVSSRFKGSGSGTEYTLTISGVQCDDAATYYCQQGYSISDIDNSFGGGTEVVVKGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC  211
                                    10        20        30        40        50        60        70        80        90     |||97       107       117       127       137       147       157       167       177       187       197       207    
                                                                                                                         95A||                                                                                                                    
                                                                                                                          95B|                                                                                                                    
                                                                                                                           95C                                                                                                                    


Chain P from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...ee.hhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                4jo3 P  321 EIIGDIRQA  329


Chain Q from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...ee.hhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                4jo3 Q  321 EIIGDIRQA  329
   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  (1, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JO3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JO3)

(-) Gene Ontology  (21, 29)

Asymmetric Unit(hide GO term definitions)

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  Q9YY05_9HIV1 | Q9YY05
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1Y2 | P35961: 1g9n 1rzk 1yyl 1yym 2i5y 2i60 2ny7 2qad 3hi1 3tgq 4dvr 4jzw 4jzz 4k0a 4ka2 4laj 4r4f 4rqs 4rwy 5a7x 5a8h

(-) Related Entries Specified in the PDB File

4jo1 4jo2 4jo4