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(-) Description

Title :  CRYSTAL STRUCTURE OF GERMLINE ANTIBODY PGT121-GL FAB
 
Authors :  L. Scharf, P. J. Bjorkman
Date :  25 Jun 12  (Deposition) - 14 Nov 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A,B,C,D,E,F,H,L
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  H,L  (1x)
Keywords :  Ig Fold, Anti Hiv, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mouquet, L. Scharf, Z. Euler, Y. Liu, C. Eden, J. F. Scheid, A. Halper-Stromberg, P. N. Gnanapragasam, D. I. Spencer, M. S. Seaman H. Schuitemaker, T. Feizi, M. C. Nussenzweig, P. J. Bjorkman
Complex-Type N-Glycan Recognition By Potent Broadly Neutralizing Hiv Antibodies.
Proc. Natl. Acad. Sci. Usa V. 109 E3268 2012
PubMed-ID: 23115339  |  Reference-DOI: 10.1073/PNAS.1217207109

(-) Compounds

Molecule 1 - FAB LIGHT CHAIN
    Chains: L, A, C, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK293-6E
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: H, B, D, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK293-6E
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFHL
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER H:177BINDING SITE FOR RESIDUE NA L 400
2AC2SOFTWARESER D:177BINDING SITE FOR RESIDUE NA D 400

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:135 -A:194
3B:22 -B:92
4B:140 -B:196
5C:23 -C:88
6C:135 -C:194
7D:22 -D:92
8D:140 -D:196
9E:23 -E:88
10E:135 -E:194
11F:22 -F:92
12F:140 -F:196
13H:22 -H:92
14H:140 -H:196
15L:23 -L:88
16L:135 -L:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Tyr L:141 -Pro L:142
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Tyr A:141 -Pro A:142
5Phe B:146 -Pro B:147
6Glu B:148 -Pro B:149
7Tyr C:141 -Pro C:142
8Phe D:146 -Pro D:147
9Glu D:148 -Pro D:149
10Tyr E:141 -Pro E:142
11Phe F:146 -Pro F:147
12Glu F:148 -Pro F:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FQQ)

(-) 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:211
                                                                                                                                                                                                                                                    
               SCOP domains d4fqqa1 A:3-108 automated matches                                                                            d4fqqa2 A:109-210 automated matches                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee.......eee...eeeee........eeeee.....hhhhh.eeeeeeeeee.....eeeeee...ee...eee...ee.....eeeeeeeeehhhhhh....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fqq A    3 YVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHPWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  210
                                    12        22        32        42        52        62        72        82        92   |||  99       109       119       129       139       149       159       169       179       189       199       209 
                                                                                                                       95A||                                                                                                                   
                                                                                                                        95B|                                                                                                                   
                                                                                                                         95C                                                                                                                   


Chain B 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.......eeeeee....eeeeee...hhhhheeeeeeeeeeeeee........eeeeeeeeee...eeeee......eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fqq B    1 QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTQQGKRIYGVVSFGDYYYYYYMDVWGKGTTVTVSSASTPSVFPLAPSSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G|||||||101       111    || 123    || 136       146       156       166       176       186       196       206       
                                                                                                            82A||               100A|||||100J||||||             116|      128|                                                                                 
                                                                                                             82B|                100B|||||100K|||||              119       132                                                                                 
                                                                                                              82C                 100C|||||100L||||                                                                                                            
                                                                                                                                   100D|||||100M|||                                                                                                            
                                                                                                                                    100E|||| 100N||                                                                                                            
                                                                                                                                     100F|||  100O|                                                                                                            
                                                                                                                                      100G||   100P                                                                                                            
                                                                                                                                       100H|                                                                                                                   
                                                                                                                                        100I                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains d4fqqc1 C:3-108 automated matches                                                                            d4fqqc2 C:109-209 automated matches                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee.......eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeee.........eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4fqq C    3 YVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHPWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  209
                                    12        22        32        42        52        62        72        82        92   |||  99       109       119       129       139       149       159       169       179       189       199       209
                                                                                                                       95A||                                                                                                                  
                                                                                                                        95B|                                                                                                                  
                                                                                                                         95C                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeeee........eeeeeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fqq D    1 QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTQQGKRIYGVFGDYYYYYYMDVWGKGTTVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100I|||||||103       113       123    || 138       148       158       168       178       188       198       208      
                                                                                                            82A||               100A|||||100L||||                         128|                                                                                
                                                                                                             82B|                100B|||||100M|||                          134                                                                                
                                                                                                              82C                 100C|||||100N||                                                                                                             
                                                                                                                                   100D|||||100O|                                                                                                             
                                                                                                                                    100G|||| 100P                                                                                                             
                                                                                                                                     100H|||                                                                                                                  
                                                                                                                                      100I||                                                                                                                  
                                                                                                                                       100J|                                                                                                                  
                                                                                                                                        100K                                                                                                                  


Chain E from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                              
               SCOP domains d4fqqe1 E:3-108 automated matches                                                                            d4fqqe2 E:109-209 automated matches                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee..hhhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee.......eee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee....ee...ee.....eeeeeeeee..........eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fqq E    3 YVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHPWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  209
                                    12        22        32        42        52        62        72        82        92   |||  99       109       119       129       139       149    || 164       174       184       194       204     
                                                                                                                       95A||                                                        154|                                                 
                                                                                                                        95B|                                                         160                                                 
                                                                                                                         95C                                                                                                             


Chain F from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeeeeee......eeeeeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee...eeeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fqq F    1 QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTQQGKRIYGVFGDYYYYYYMDVWGKGTTVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100I|||||||103       113       123   ||  139       149       159       169       179       189       199       209      
                                                                                                            82A||               100A|||||100L||||                        127|                                                                                 
                                                                                                             82B|                100B|||||100M|||                         134                                                                                 
                                                                                                              82C                 100C|||||100N||                                                                                                             
                                                                                                                                   100D|||||100O|                                                                                                             
                                                                                                                                    100G|||| 100P                                                                                                             
                                                                                                                                     100H|||                                                                                                                  
                                                                                                                                      100I||                                                                                                                  
                                                                                                                                       100J|                                                                                                                  
                                                                                                                                        100K                                                                                                                  


Chain H from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeeeeeeee..hhhhh.eeeeeeeeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4fqq H    1 QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTQQGKRIYGVVSFGDYYYYYYMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G|||||||101       111       121       131       141       151       161       171       181       191       201       211    
                                                                                                            82A||               100A|||||100J||||||                                                                                                                   
                                                                                                             82B|                100B|||||100K|||||                                                                                                                   
                                                                                                              82C                 100C|||||100L||||                                                                                                                   
                                                                                                                                   100D|||||100M|||                                                                                                                   
                                                                                                                                    100E|||| 100N||                                                                                                                   
                                                                                                                                     100F|||  100O|                                                                                                                   
                                                                                                                                      100G||   100P                                                                                                                   
                                                                                                                                       100H|                                                                                                                          
                                                                                                                                        100I                                                                                                                          


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d4fqql1 L:3-108 automated matches                                                                            d4fqql2 L:109-212 automated matches                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhh...............................................hhhhh.........................................hhhhhhh.....................................................hhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fqq L    3 YVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHPWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  212
                                    12        22        32        42        52        62        72        82        92   |||  99       109       119       129       139       149       159       169       179       189       199       209   
                                                                                                                       95A||                                                                                                                     
                                                                                                                        95B|                                                                                                                     
                                                                                                                         95C
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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  (2, 8)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

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  4fqq
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  Q8N355_HUMAN | Q8N355
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8N355_HUMAN | Q8N355: 2dd8 5ugy
UniProtKB/TrEMBL
        Q6GMX6_HUMAN | Q6GMX6: 1bey 1za6 2jix 3b2u 3b2v 3d0l 3zl4 4d9l 4lkx 4npy 4qhk 4qhl 4qhm 4qhn
        Q8N355_HUMAN | Q8N355: 4hk0 4hk3

(-) Related Entries Specified in the PDB File

4fq1 4fq2 4fqc