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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ANTI-HIV-1 GP120-REACTIVE ANTIBODY E51
 
Authors :  C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, M. Farzan, P. D. Kwong
Date :  24 Dec 03  (Deposition) - 03 Feb 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Hiv-1; Gp120; Cd4I; Antibodies; Tyrosine Sulfation; Vh-Gene Usage, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, H. Choe, M. Farzan, P. D. Kwong
Structural Basis Of Tyrosine Sulfation And Vh-Gene Usage In Antibodies That Recognize The Hiv Type 1 Coreceptor-Binding Site On Gp120
Proc. Natl. Acad. Sci. Usa V. 101 2706 2004
PubMed-ID: 14981267  |  Reference-DOI: 10.1073/PNAS.0308527100

(-) Compounds

Molecule 1 - FAB E51 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HUMAN HERPESVIRUS 4
    Expression System Cell: IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
    Expression System Common: EPSTEIN-BARR VIRUS
    Expression System Taxid: 10376
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB E51 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HUMAN HERPESVIRUS 4
    Expression System Cell: IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
    Expression System Common: EPSTEIN-BARR VIRUS
    Expression System Taxid: 10376
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1GOL13Ligand/IonGLYCEROL
2IPA2Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS H:209 , ALA L:113 , HIS L:198 , SER L:201 , HOH L:9050 , HOH L:9054 , HOH L:9154BINDING SITE FOR RESIDUE GOL L 9001
02AC2SOFTWAREGLN L:37 , LYS L:45 , PRO L:59 , ARG L:61 , PHE L:62 , GLY L:81 , ASP L:82BINDING SITE FOR RESIDUE GOL L 9002
03AC3SOFTWARETHR H:183 , SER L:115 , THR L:117 , LEU L:136 , ILE L:137 , SER L:138BINDING SITE FOR RESIDUE GOL L 9003
04AC4SOFTWARETHR L:105 , VAL L:106 , LEU L:107 , GLY L:108 , GLN L:109 , LYS L:111 , PRO L:142BINDING SITE FOR RESIDUE GOL L 9004
05AC5SOFTWAREALA L:144 , VAL L:145 , THR L:146 , THR L:197 , GLU L:199 , GLY L:200 , HOH L:9061BINDING SITE FOR RESIDUE GOL L 9005
06AC6SOFTWARESER H:172 , ARG L:54 , PRO L:55 , SER L:56 , GLY L:57 , ILE L:58 , GLY L:159 , VAL L:160 , GLU L:161 , HOH L:9159BINDING SITE FOR RESIDUE GOL L 9010
07AC7SOFTWAREPRO L:110 , TYR L:141 , ASN L:171 , HOH L:9067BINDING SITE FOR RESIDUE GOL L 9011
08AC8SOFTWAREILE H:53 , SER L:65 , LYS L:66 , SER L:67 , SER L:70 , ALA L:71 , THR L:72BINDING SITE FOR RESIDUE GOL L 9012
09AC9SOFTWAREPHE H:54 , LYS L:18 , THR L:20 , SER L:63 , GLY L:64 , SER L:65 , HOH L:9106BINDING SITE FOR RESIDUE GOL L 9013
10BC1SOFTWAREGLN L:38 , GLY L:41BINDING SITE FOR RESIDUE IPA L 7001
11BC2SOFTWAREGLN H:43 , GLY H:44 , ASP L:85 , TYR L:87 , GLY L:100BINDING SITE FOR RESIDUE IPA L 7002
12BC3SOFTWAREGLY H:100L , TYR H:100O , ASP H:100P , HOH H:9020 , ASP L:32 , SER L:34 , TYR L:36 , GLY L:89 , THR L:90 , VAL L:96BINDING SITE FOR RESIDUE GOL H 9006
13BC4SOFTWARESER H:120 , VAL H:121 , LYS H:209 , HOH H:9166 , SER L:201 , VAL L:203 , HOH L:9054BINDING SITE FOR RESIDUE GOL H 9007
14BC5SOFTWAREARG H:38 , GLN H:39 , ALA H:40 , GLN H:43 , GLY H:44 , GLU H:46 , HOH H:9062BINDING SITE FOR RESIDUE GOL H 9008
15BC6SOFTWARELEU H:45 , GLU H:46 , HOH H:9010 , HOH H:9014 , HOH H:9108BINDING SITE FOR RESIDUE GOL H 9009

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:135 -L:194

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr L:141 -Pro L:142
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RZF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RZF)

(-) Exons   (0, 0)

(no "Exon" information available for 1RZF)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1rzfh1 H:2-113 Immunoglobulin heavy chain variable domain, VH                                                           d1rzfh2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 1rzfH01 H:2-110 Immunoglobulins                                                                                       1rzfH02 H:111-214 Immunoglobulins                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee.......eeeeeeee.....eeeeeeeehhhheeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..........ee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rzf H    2 VQLVQSGAEVNKPGSSVKVSCQASGATLNSHAFSWVRQAPGQGLEWMAGIIPIFGSSHYAQKFRGRVTISADESTRTVYLHLRGLRSDDTAVYYCASNSIAGGYYYDMDVWGQGTTVTVSSASTKGPSVFPLAPTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    11        21        31        41        51 |      60        70        80  |||   87        97|||||||102       112       122   ||  136       146       156       166       176       186       196       206        
                                                                             52A                            82A||              98|||||||                       126|                                                                                   
                                                                                                             82B|             100K||||||                        131                                                                                   
                                                                                                              82C              100L|||||                                                                                                              
                                                                                                                                100M||||                                                                                                              
                                                                                                                                 100N|||                                                                                                              
                                                                                                                                  100O||                                                                                                              
                                                                                                                                   100P|                                                                                                              
                                                                                                                                    100Q                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1rzfl1 L:2-108 Immunoglobulin light chain lambda variable domain, VL-lambda                                   d1rzfl2 L:109-210 Immunoglobulin light chain lambda constant domain, CL-lambda                         SCOP domains
               CATH domains -1rzfL01 L:3-108 Immunoglobulins                                                                               1rzfL02 L:109-209 Immunoglobulins                                                                    - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rzf L    2 QSILTQPPSVSAAPGQKVTISCSGSSSNIGNNDVSWYQQFPGTVPKLVIYENNERPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAVVFGGGSKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  210
                                    11        21      ||29        39        49        59        69        79        89      ||97       107       117       127       137       147       157       167       177       187       197       207   
                                                    27A|                                                                  95A|                                                                                                                   
                                                     27B                                                                   95B
   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  (4, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RZF)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1RZF)

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  1rzf
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 Related Entries

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(-) Related Entries Specified in the PDB File

1rz7 1rz8 1rzg 1rzi 1rzj 1rzk