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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FAB PGT124, A BROADLY NEUTRALIZING AND POTENT HIV-1 NEUTRALIZING ANTIBODY
 
Authors :  F. Garces, L. Kong, I. A. Wilson
Date :  08 Aug 14  (Deposition) - 08 Oct 14  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immune System, Igg Fold, Antibody, Hiv-1 Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Garces, D. Sok, L. Kong, R. Mcbride, H. J. Kim, K. F. Saye-Francisco, J. P. Julien, Y. Hua, A. Cupo, J. P. Moore, J. C. Paulson, A. B. Ward, D. R. Burton, I. A. Wilson
Structural Evolution Of Glycan Recognition By A Family Of Potent Hiv Antibodies.
Cell(Cambridge, Mass. ) V. 159 69 2014
PubMed-ID: 25259921  |  Reference-DOI: 10.1016/J.CELL.2014.09.009

(-) Compounds

Molecule 1 - PGR124-LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293F
    Expression System Taxid: 9606
    Gene: IGLC3
    Organism Common: NORTHERN WHITE-CHEEKED GIBBON, HUMAN
    Organism Scientific: NOMASCUS LEUCOGENYS, HOMO SAPIENS
    Organism Taxid: 61853, 9606
    Synonym: IG LAMBDA CHAIN C REGION DOT,IG LAMBDA CHAIN C REGION NEWM, IG LAMBDA-3 CHAIN C REGIONS
 
Molecule 2 - PGT124-HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293F
    Expression System Taxid: 9606
    Gene: IGH@
    Organism Common: HUMAN, HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IMMUNOGLOBULIN GAMMA-1 HEAVY CHAIN NIE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN L:37 , ILE L:45 , PRO L:59 , PHE L:62 , GLY L:81 , ASP L:82 , HOH L:441BINDING SITE FOR RESIDUE GOL L 301
2AC2SOFTWARETHR L:105 , LEU L:106A , TYR L:140 , GLY L:142 , TYR L:172BINDING SITE FOR RESIDUE GOL L 302
3AC3SOFTWARELEU L:15 , GLY L:16 , GLU L:17BINDING SITE FOR RESIDUE GOL L 303

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:193

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr L:140 -Pro L:141
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Ser H:161 -Gly H:162
5Ser H:203 -Asn H:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R26)

(-) Exons   (0, 0)

(no "Exon" information available for 4R26)

(-) 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:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeeeeeee........eeeeee........eeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r26 H    2 VQLQESGPGLVRPSETLSVTCIVSGGSISNYYWTWIRQSPGKGLEWIGYISDRETTTYNPSLNSRAVISRDTSKNQLSLQLRSVTTADTAIYFCATARRGQRIYGVVSFGEFFYYYYMDVWGKGTAVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    11        21        31        41        51        61        71        81 |||    88        98  ||||100H|||||||102       112       122   ||  137       147       157       167       177       187       197       207      
                                                                                                           82A||               100A|||||100J||||||                       126|                                                                                 
                                                                                                            82B|                100B|||||100K|||||                        132                                                                                 
                                                                                                             82C                 100C|||||100L||||                                                                                                            
                                                                                                                                  100D|||||100M|||                                                                                                            
                                                                                                                                   100E|||| 100N||                                                                                                            
                                                                                                                                    100F|||  100O|                                                                                                            
                                                                                                                                     100G||   100P                                                                                                            
                                                                                                                                      100H|                                                                                                                   
                                                                                                                                       100I                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee....eeee.........eeeeeee......eeee.............ee...........eeee...hhhhheeeeeeee............eeeeeee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhh....eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4r26 L    5 YVSPLSVALGETARISCGRQALGSRAVQWYQHKPGQAPILLIYNNQDRPSGIPERFSGTPDINFGTTATLTISGVEVGDEADYYCHMWDSRSGFSWSFGGATRLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  209
                               ||   16        26        36        46        56        66|||     73        83        93  |||  100      |109       119       129       139       149       159       169       179       189       199       209
                               8|                                                     66A||                           95A||        106A                                                                                                       
                               11                                                      66B|                            95B|                                                                                                                   
                                                                                        66C                             95C
   Legend:   → Mismatch (orange background)
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  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 4R26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R26)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4R26)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser H:161 - Gly H:162   [ RasMol ]  
    Ser H:203 - Asn H:204   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  4r26
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGG1_HUMAN | P0DOX5: 1d5b 1d5i 1d6v 1hzh 1n0x 3pgf 4r2g 5vj6
        IGLC3_HUMAN | P0DOY3: 1aqk 3tv3 3twc 3tyg 4lld 4llm 4o58 4o5i 4o5l 4r2g 5d9q 5iq7 5iq9 7fab

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4R26)