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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB 32H+109L, A PUTATIVE PRECURSOR OF THE PGT121 FAMILY OF POTENT HIV-1 ANTIBODIES
 
Authors :  F. Garces, I. A. Wilson
Date :  07 Jul 15  (Deposition) - 23 Dec 15  (Release) - 06 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hiv-1, Immune System, Antibody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Garces, J. H. Lee, N. De Val, A. Torrents De La Pena, L. Kong, C. Puchades, Y. Hua, R. L. Stanfield, D. R. Burton, J. P. Moore, R. W. Sanders, A. B. Ward, I. A. Wilson
Affinity Maturation Of A Potent Family Of Hiv Antibodies Is Primarily Focused On Accommodating Or Avoiding Glycans.
Immunity V. 43 1053 2015
PubMed-ID: 26682982  |  Reference-DOI: 10.1016/J.IMMUNI.2015.11.007

(-) Compounds

Molecule 1 - ANTIBODY 9H+3L FAB LIGHT CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTIBODY 9H+3L FAB HEAVY CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2P6G2Ligand/IonHEXAETHYLENE GLYCOL
3PG43Ligand/IonTETRAETHYLENE GLYCOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:49 , GLN A:52 , ASP A:53 , ARG A:54 , ASN C:50 , HIS D:97 , GLY D:98 , ARG D:99 , TYR D:100M , HOH D:314binding site for residue PG4 A 301
02AC2SOFTWAREGLU B:146 , PRO B:147 , VAL B:148 , PRO B:165 , ALA B:166binding site for residue GOL B 301
03AC3SOFTWAREPRO B:41 , ILE B:89 , TYR B:91 , PRO B:106 , THR B:108 , GLU B:146 , TYR B:174binding site for residue P6G B 302
04AC4SOFTWAREGLN C:38 , PRO C:40 , ALA C:84 , ASP C:85 , LYS C:103binding site for residue GOL C 301
05AC5SOFTWAREPRO C:59 , ARG C:61 , GLU C:79binding site for residue GOL C 302
06AC6SOFTWAREHIS B:32 , GLN B:96 , ASP C:53 , ARG C:54binding site for residue GOL C 303
07AC7SOFTWAREGLN C:37 , LYS C:39 , PRO C:40 , GLN C:42 , PHE C:62 , GLY C:81 , ASP C:82 , GLN C:168binding site for residue P6G C 304
08AC8SOFTWARESER A:56 , VAL C:45 , LEU C:46 , PRO C:55 , SER C:56 , ILE C:58 , PG4 C:306 , HOH C:439 , ASP D:100Qbinding site for residue PG4 C 305
09AC9SOFTWARESER A:56 , ILE A:58 , VAL B:2 , ARG C:54 , SER C:56 , GLY C:57 , PG4 C:305binding site for residue PG4 C 306
10AD1SOFTWAREGLN C:195 , THR C:202 , GLU C:204binding site for residue PGE C 307

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:135 -A:194
3B:138 -B:194
4C:23 -C:88
5C:135 -C:194
6D:22 -D:92
7D:138 -D:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Tyr A:141 -Pro A:142
2Phe B:144 -Pro B:145
3Glu B:146 -Pro B:147
4Tyr C:141 -Pro C:142
5Glu D:146 -Pro D:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CEX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CEX)

(-) Exons   (0, 0)

(no "Exon" information available for 5CEX)

(-) 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:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....eeee........eeeeeeee......eeee.............eee......eeee...hhhhh.eeeeeeee............eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cex A    6 TQPSQLSVAPGETARISCGGRSLGSRAVQWYQQKPGQAPVLVIYNNQDRPSGIPERFSGSPDTTATLTISRVEAGDEADYYCHMWDSRSAINWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  210
                                    15        25        35        45        55        65 ||     76        86       95A||     103       113       123       133       143       153       163       173       183       193       203       
                                                                                        67|                        95A||                                                                                                                   
                                                                                         69                         95B|                                                                                                                   
                                                                                                                     95C                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeeeeee..hhhhh.eeeeeeeeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhhh.eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cex B    1 QVQLQESGPGLVKPSETLSLTCSVSGASISDHYWSWIRQSPGKGLEWIGYVYDSGDTNYNPSLKSRVNLSLDTSKNQVSLSLTAVTAADSAIYYCARTQHGRRIYGIVAFREWFTYFYMDVWGQGTPVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  212
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G||||||100Q|      109       119       129       139       149       159       169       179       189       199       209   
                                                                                                            82A||               100A|||||100J||||||||                                                                                                                
                                                                                                             82B|                100B|||||100K|||||||                                                                                                                
                                                                                                              82C                 100C|||||100L||||||                                                                                                                
                                                                                                                                   100D|||||100M|||||                                                                                                                
                                                                                                                                    100E|||| 100N||||                                                                                                                
                                                                                                                                     100F|||  100O|||                                                                                                                
                                                                                                                                      100G||   100P||                                                                                                                
                                                                                                                                       100H|    100Q|                                                                                                                
                                                                                                                                        100I     100R                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeee........eeeeeeee......eeee.............eee..........eeee...hhhhheeeeeeeee............eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cex C    5 LTQPSQLSVAPGETARISCGGRSLGSRAVQWYQQKPGQAPVLVIYNNQDRPSGIPERFSGSPDSNFGTTATLTISRVEAGDEADYYCHMWDSRSAINWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTE  211
                                    14        24        34        44        54        64   |||  71        81        91    ||| 98       108       118       128       138       148       158       168       178       188       198       208   
                                                                                         67A||                          95A||                                                                                                                    
                                                                                          67B|                           95B|                                                                                                                    
                                                                                           67C                            95C                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeeeeeeee........eeeeeeeeee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cex D    1 QVQLQESGPGLVKPSETLSLTCSVSGASISDHYWSWIRQSPGKGLEWIGYVYDSGDTNYNPSLKSRVNLSLDTSKNQVSLSLTAVTAADSAIYYCARTQHGRRIYGIVAFREWFTYFYMDVWGQGTPVTVSSASTKGPSVFPLAPSSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  213
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G||||||100Q|      109       119      |131       141       151       161       171       181       191       201       211  
                                                                                                            82A||               100A|||||100J||||||||                       126|                                                                                    
                                                                                                             82B|                100B|||||100K|||||||                        129                                                                                    
                                                                                                              82C                 100C|||||100L||||||                                                                                                               
                                                                                                                                   100D|||||100M|||||                                                                                                               
                                                                                                                                    100E|||| 100N||||                                                                                                               
                                                                                                                                     100F|||  100O|||                                                                                                               
                                                                                                                                      100G||   100P||                                                                                                               
                                                                                                                                       100H|    100Q|                                                                                                               
                                                                                                                                        100I     100R
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  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 5CEX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CEX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CEX)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5CEX)

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  5cex
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 Related Entries

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(-) Related Entries Specified in the PDB File

5cey 5cez