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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB 9H+3L, A PUTATIVE PRECURSOR OF THE PGT121 FAMILY OF POTENT HIV-1 ANTIBODIES
 
Authors :  I. A. Wilson, F. Garces
Date :  07 Jul 15  (Deposition) - 23 Dec 15  (Release) - 06 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hiv-1, Antibody, Immune System (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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3PE71Ligand/Ion1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3PE7-1Ligand/Ion1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2P6G-1Ligand/IonHEXAETHYLENE GLYCOL
3PE71Ligand/Ion1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:60 , TYR A:141 , PRO A:142 , GLY A:143 , ALA A:144 , TYR A:173binding site for residue GOL A 301
2AC2SOFTWARESER A:191 , THR A:206 , SER B:70 , LYS B:81binding site for residue P6G B 301
3AC3SOFTWAREGLY C:41 , GLY D:104 , PRO D:147binding site for residue GOL C 301
4AC4SOFTWARESER C:153 , THR C:206 , ARG D:66 , VAL D:68 , SER D:70 , LYS D:81 , ASN D:82Abinding site for residue PE7 D 301

(-) SS Bonds  (6, 6)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Tyr A:141 -Pro A:142
2Lys B:127 -Ser B:128
3Phe B:144 -Pro B:145
4Glu B:146 -Pro B:147
5Ser B:201 -Asn B:202
6Tyr C:141 -Pro C:142
7Phe D:144 -Pro D:145
8Glu D:146 -Pro D:147
9Ser D:159 -Gly D:160
10Ser D:201 -Asn D:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CEY)

(-) 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeee........eeeeeeee......eeee.............eee..........eeee...hhhhheeeeeeeee...........eeeeeee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cey A    6 SYVRPLSVALGETASISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERFSGTPDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  210
                                    15        25        35        45        55        65  |||   72        82        92   |||  99       109       119       129       139       149       159       169       179       189       199       209 
                                                                                        67A||                          95A||                                                                                                                   
                                                                                         67B|                           95B|                                                                                                                   
                                                                                          67C                            95C                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeeee....hhhhh.eeeeeeeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeee..........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cey B    1 QVQLQESGPGLVKPSETLSVTCIVSGGSISNYYWTWIRQSPGKGLEWIGYISDRETTTYNPSLKSRVVISRDTSKNQLSLKLNSVTAADTAIYYCATARRGQRIYGVVSFGEFFYYYYMDVWGKGTAVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  211
                                    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:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeee........eeeeeeee......eeee.............eee.......eeee...hhhhheeeeeeeee...........eeeeeee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhh....eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cey C    7 YVRPLSVALGETASISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERFSGTPDINRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  210
                                    16        26        36        46        56        66 |||    76        86       95A||     103       113       123       133       143       153       163       173       183       193       203       
                                                                                       67A||                       95A||                                                                                                                   
                                                                                        67B|                        95B|                                                                                                                   
                                                                                          70                         95C                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeeeeee............eeeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhhhh.eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cey D    2 VQLQESGPGLVKPSETLSVTCIVSGGSISNYYWTWIRQSPGKGLEWIGYISDRETTTYNPSLKSRVVISRDTSKNQLSLKLNSVTAADTAIYYCATARRGQRIYGVVSFGEFFYYYYMDVWGKGTAVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  211
                                    11        21        31        41        51        61        71        81 |||    88        98  ||||100H||||||100R       110       120    || 136       146       156       166       176       186       196       206     
                                                                                                           82A||               100A|||||100J||||||||                      125|                                                                               
                                                                                                            82B|                100B|||||100K|||||||                       132                                                                               
                                                                                                             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 5CEY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  5cey
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5cex ANTIBODY OF THE SAME FAMILY
5cez