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(-) Description

Title :  CRYSTAL STRUCTURE OF 3BNC60 FAB WITH P61A MUTATION
 
Authors :  R. Diskin, B. Z. Fu, P. J. Bjorkman
Date :  31 Aug 12  (Deposition) - 17 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Fwr, Igg, Anti Hiv, Gp120, Hiv, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Klein, R. Diskin, J. F. Scheid, C. Gaebler, H. Mouquet, I. S. Georgiev, M. Pancera, T. Zhou, R. B. Incesu, B. Z. Fu, P. N. Gnanapragasam, T. Y. Oliveira, M. S. Seaman, P. D. Kwong, P. J. Bjorkman, M. C. Nussenzweig
Somatic Mutations Of The Immunoglobulin Framework Are Generally Required For Broad And Potent Hiv-1 Neutralization.
Cell(Cambridge, Mass. ) V. 153 126 2013
PubMed-ID: 23540694  |  Reference-DOI: 10.1016/J.CELL.2013.03.018

(-) Compounds

Molecule 1 - 3BNC60 FAB LIGHT-CHAIN
    Chains: L, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293-6E
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 3BNC60 FAB HEAVY-CHAIN
    Chains: H, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293-6E
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA-1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR L:22 , ARG L:63 , TRP L:65 , ASN L:70 , HOH L:452BINDING SITE FOR RESIDUE NAG L 301
2AC2SOFTWARETHR B:20 , THR B:22 , TRP B:65 , ASN B:70 , HOH B:432BINDING SITE FOR RESIDUE NAG B 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:146 -A:202
3B:23 -B:86
4B:123 -B:183
5H:22 -H:96
6H:146 -H:202
7L:23 -L:86
8L:123 -L:183

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:129 -Pro L:130
3Phe H:152 -Pro H:153
4Glu H:154 -Pro H:155
5Phe A:152 -Pro A:153
6Glu A:154 -Pro A:155
7Ser B:7 -Pro B:8
8Tyr B:129 -Pro B:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GW4)

(-) Exons   (0, 0)

(no "Exon" information available for 4GW4)

(-) 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 A from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeee.....eeeeeeee...hhhhheeeeeee.........ee...eeeee........eeeee...eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee..hhhhhh..eeeeehhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gw4 A   2 VHLSQSGAAVTKPGASVRVSCEASGYKISDHFIHWWRQAPGQGLQWVGWINPKTGQPNNARQFQGRVSLTRQASWDFDTYSFYMDLKAVRSDDTAIYFCARQRSDFWDFDVWGSGTQVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRV 217
                                    11        21        31        41        51        61        71   |||  78|       87        97       107       117       127    || 145       155       165       175       185       195       205       215  
                                                                                                   74A||  78A                                                   132|                                                                            
                                                                                                    74B|                                                         141                                                                            
                                                                                                     74C                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains d4gw4b1 B:4-96 automated matches                                                                d4gw4b2 B:97-199 automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeee.....eeeeee.....eeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh..eeeeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gw4 B   4 MTQSPSSLSARVGDTVTITCQANGYLNWYQQRRGKAPKLLIYDGSKLERGVPARFSGRRWGQEYNLTINNLQPEDVATYFCQVYEFIVPGTRLDLKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFN 199
                                    13        23  ||  | 36  |     45        55        65        75        85     ||90E       100       110       120       130       140       150       160       170       180       190         
                                                 26|  |   38A                                                  90A||||                                                                                                             
                                                  31  |                                                         90B|||                                                                                                             
                                                    33A                                                          90C||                                                                                                             
                                                                                                                  90D|                                                                                                             
                                                                                                                   90E                                                                                                             


Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeee.....eeeeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee...eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee..hhhhhh..eeeeehhhhh...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gw4 H   1 xVHLSQSGAAVTKPGASVRVSCEASGYKISDHFIHWWRQAPGQGLQWVGWINPKTGQPNNARQFQGRVSLTRQASWDFDTYSFYMDLKAVRSDDTAIYFCARQRSDFWDFDVWGSGTQVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRV 217
                            |       10        20        30        40        50        60        70    ||| 77 |      86        96       106       116       126     ||144       154       164       174       184       194       204       214   
                            1-PCA                                                                   74A||  78A                                                   132|                                                                            
                                                                                                     74B|                                                         141                                                                            
                                                                                                      74C                                                                                                                                        


Chain L from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4gw4l1 L:4-96 automated matches                                                                d4gw4l2 L:97-198 automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee..eeee.....eeeeee.....eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhhh.eeeeeee......eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gw4 L   4 MTQSPSSLSARVGDTVTITCQANGYLNWYQQRRGKAPKLLIYDGSKLERGVPARFSGRRWGQEYNLTINNLQPEDVATYFCQVYEFIVPGTRLDLKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF 198
                                    13        23  ||  | 36  |     45        55        65        75        85     ||90E       100       110       120       130       140       150       160       170       180       190        
                                                 26|  |   38A                                                  90A||||                                                                                                            
                                                  31  |                                                         90B|||                                                                                                            
                                                    33A                                                          90C||                                                                                                            
                                                                                                                  90D|                                                                                                            
                                                                                                                   90E
   Legend:   → Mismatch (orange background)
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    → 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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GW4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GW4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4GW4)

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