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(-) Description

Title :  CRYSTAL STRUCTURE OF RABBIT MAB R56 FAB IN COMPLEX WITH V3 CROWN OF HIV-1 JR-FL 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 :  2.03
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 R56 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 R56 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) CROWN (UNP RESIDUES 32-54)
    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, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:47 , PHE L:98BINDING SITE FOR RESIDUE CA L 301
2AC2SOFTWAREPRO L:8 , SER L:9BINDING SITE FOR RESIDUE CA L 302
3AC3SOFTWARETYR H:59BINDING SITE FOR RESIDUE CA H 301
4AC4SOFTWARETRP I:47 , PHE M:98BINDING SITE FOR RESIDUE CA M 301
5AC5SOFTWARETYR I:59BINDING SITE FOR RESIDUE CA I 301

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:35A-H:50
3H:128 -H:213
4H:140 -H:193
5I:22 -I:92
6I:35A-I:50
7I:128 -I:213
8I:140 -I:193
9L:23 -L:88
10L:80 -L:170
11L:94 -L:95D
12L:134 -L:193
13L:211 -H:127
14M:23 -M:88
15M:80 -M:170
16M:94 -M:95D
17M:134 -M:193
18M:211 -I:127

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Thr L:7 -Pro L:8
2Phe L:140 -Pro L:141
3Pro H:132 -Ser H:133
4Leu H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Thr M:7 -Pro M:8
7Phe M:140 -Pro M:141
8Leu I:146 -Pro I:147
9Glu I:148 -Pro I:149
10Ser I:211 -Thr I:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JO1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JO1)

(-) Exons   (0, 0)

(no "Exon" information available for 4JO1)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeeee.....eeeeeeee......eee.......eeeeeee..eeeeee...hhhhheeeeeee...ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jo1 H   2 QSLEESGGDLVQPGASLTLTCKASGFSFGNNYDMCWVRQAPGKGLEWIGCIETGSSDSAAYATWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARNFDLWGPGTLVIVSSGQPKAPSVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAPSTC 213
                                    11        21        31    |   40        50  ||    58        68        78    ||  86        96|      110       120       130       140       150       160       170       180       190       200       210   
                                                            35A               52A|                            82A|            96|                                                                                                                
                                                                               52B                             82B            101                                                                                                                


Chain I from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeeee.....eeeeeeee......eee.......eeeeeee..eeeeee...hhhhheeeeeee...ee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee......eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jo1 I   2 QSLEESGGDLVQPGASLTLTCKASGFSFGNNYDMCWVRQAPGKGLEWIGCIETGSSDSAAYATWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARNFDLWGPGTLVIVSSGQPKAPSVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAPSTC 213
                                    11        21        31    |   40        50  ||    58        68        78    ||  86        96|      110       120       130       140       150       160       170       180       190       200       210   
                                                            35A               52A|                            82A|            96|                                                                                                                
                                                                               52B                             82B            101                                                                                                                


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d4jo1l1 L:2-108 automated matches                                                                                d4jo1l2 L:109-211 automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee...hhhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee........eee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jo1 L   2 QVLTQTPSSVSTAVGSAVTINCQSSQNVYSNNNLAWFQQKPGQPPRLLIYDASKLASGVPSRFKGSGSGTQFTFTISDVQCDDAATFYCLGGYDCSSGDCAAFGGGTEVVVRGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC 211
                                    11        21      ||29        39        49        59        69        79        89      |95D       105       115       125       135       145       155       165       175       185       195       205      
                                                    27A|                                                                  95A|||                                                                                                                    
                                                     27B                                                                   95B||                                                                                                                    
                                                                                                                            95C|                                                                                                                    
                                                                                                                             95D                                                                                                                    


Chain M from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d4jo1m1 M:2-108 automated matches                                                                                d4jo1m2 M:109-211 automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee...hhhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee........eee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jo1 M   2 QVLTQTPSSVSTAVGSAVTINCQSSQNVYSNNNLAWFQQKPGQPPRLLIYDASKLASGVPSRFKGSGSGTQFTFTISDVQCDDAATFYCLGGYDCSSGDCAAFGGGTEVVVRGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC 211
                                    11        21      ||29        39        49        59        69        79        89      |95D       105       115       125       135       145       155       165       175       185       195       205      
                                                    27A|                                                                  95A|||                                                                                                                    
                                                     27B                                                                   95B||                                                                                                                    
                                                                                                                            95C|                                                                                                                    
                                                                                                                             95D                                                                                                                    


Chain P from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4jo1 P 303 TRKSIHIGPG 314
                                  |314
                                309|  
                                 312  


Chain Q from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4jo1 Q 303 TRKSIHIGPG 314
                                  |314
                                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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JO1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JO1)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4jo2 4jo3 4jo4