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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-SARS M396 ANTIBODY
 
Authors :  P. Prabakaran, J. H. Gan, Y. Feng, Z. Y. Zhu, X. D. Xiao, X. Ji, D. S. Dimitr
Date :  27 Feb 06  (Deposition) - 04 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Sars, S Protein, Antibody, Epitopes, Vaccines, Inhibitors, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Prabakaran, J. Gan, Y. Feng, Z. Zhu, V. Choudhry, X. Xiao, X. Ji, D. S. Dimitrov
Structure Of Severe Acute Respiratory Syndrome Coronavirus Receptor-Binding Domain Complexed With Neutralizing Antibody.
J. Biol. Chem. V. 281 15829 2006
PubMed-ID: 16597622  |  Reference-DOI: 10.1074/JBC.M600697200

(-) Compounds

Molecule 1 - IGG HEAVY CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDZ1.0
    Expression System Strain: HB2151
    Expression System Taxid: 562
    Expression System Vector Type: PHAGEMID
    Fragment: FAB M396, HEAVY CHAIN
    Gene: RECOMBINANT ANTIBODY FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - IGG LIGHT CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDZ1.0
    Expression System Strain: HB2151
    Expression System Taxid: 562
    Expression System Vector Type: PHAGEMID
    Fragment: FAB M396, LIGHT CHAIN
    Gene: RECOMBINANT ANTIBODY FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2G75)

(-) Sites  (0, 0)

(no "Site" information available for 2G75)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:135 -B:194
5C:22 -C:92
6C:140 -C:196
7D:23 -D:88
8D:135 -D:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Tyr B:141 -Pro B:142
4Phe C:146 -Pro C:147
5Glu C:148 -Pro C:149
6Tyr D:141 -Pro D:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G75)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G75)

(-) Exons   (0, 0)

(no "Exon" information available for 2G75)

(-) 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:218
                                                                                                                                                                                                                                                           
               SCOP domains d2g75a1 A:2-113 Immunoglobulin heavy chain variable domain, VH                                                       d2g75a2 A:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 2g75A01 A:2-113 Immunoglobulins                                                                                      2g75A02 A:114-214 Immunoglobulins                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee.........eeeeee.....eeeeeee......eee.......eeeee.....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2g75 A    2 VQLQQSGAEVKKPGSSVKVSCKASGGTFSSYTISWVRQAPGQGLEWMGGITPILGIANYAQKFQGRVTITTDESTSTAYMELSSLRSEDTAVYYCARDTVMGGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTSALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    11        21        31        41        51 |      60        70        80  |||   87        97   |   106       116       126       136       146       156       166       176       186       196       206        
                                                                             52A                            82A||               100A                                                                                                                  
                                                                                                             82B|                                                                                                                                     
                                                                                                              82C                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d2g75b1 B:2-108 Immunoglobulin light chain lambda variable domain, VL-lambda                                d2g75b2 B:109-211 Immunoglobulin light chain lambda constant domain, CL-lambda                          SCOP domains
               CATH domains 2g75B01 B:2-108 Immunoglobulins                                                                             2g75B02 B:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee...eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2g75 B    2 SYELTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDYVFGTGTKVTVLGQPKANPTVTLFPPSSEEFQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE  211
                                    11        21        31        41        51        61        71        81        91    |  100       110       120       130       140       150       160       170       180       190       200       210 
                                                                                                                        95A                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d2g75c1 C:2-113 Immunoglobulin heavy chain variable domain, VH                                                       d2g75c2 C:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 2g75C01 C:2-113 Immunoglobulins                                                                                      2g75C02 C:114-214 Immunoglobulins                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee.........eeeeee......eeeeeee....eeee.......eeeee.....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2g75 C    2 VQLQQSGAEVKKPGSSVKVSCKASGGTFSSYTISWVRQAPGQGLEWMGGITPILGIANYAQKFQGRVTITTDESTSTAYMELSSLRSEDTAVYYCARDTVMGGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTSALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    11        21        31        41        51 |      60        70        80  |||   87        97   |   106       116       126       136       146       156       166       176       186       196       206        
                                                                             52A                            82A||               100A                                                                                                                  
                                                                                                             82B|                                                                                                                                     
                                                                                                              82C                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d2g75d1 D:2-108 Immunoglobulin light chain lambda variable domain, VL-lambda                                d2g75d2 D:109-211 Immunoglobulin light chain lambda constant domain, CL-lambda                          SCOP domains
               CATH domains 2g75D01 D:2-108 Immunoglobulins                                                                             2g75D02 D:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee...eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2g75 D    2 SYELTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDYVFGTGTKVTVLGQPKANPTVTLFPPSSEEFQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE  211
                                    11        21        31        41        51        61        71        81        91    |  100       110       120       130       140       150       160       170       180       190       200       210 
                                                                                                                        95A
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (4, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a2g75A02A:114-214
1b2g75C02C:114-214
1c2g75B01B:2-108
1d2g75D01D:2-108
1e2g75A01A:2-113
1f2g75C01C:2-113
1g2g75B02B:109-211
1h2g75D02D:109-211

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G75)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2G75)

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  Cis Peptide Bonds
    Glu A:148 - Pro A:149   [ RasMol ]  
    Glu C:148 - Pro C:149   [ RasMol ]  
    Phe A:146 - Pro A:147   [ RasMol ]  
    Phe C:146 - Pro C:147   [ RasMol ]  
    Tyr B:141 - Pro B:142   [ RasMol ]  
    Tyr D:141 - Pro D:142   [ RasMol ]  
 
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  2g75
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1za6 THE STRUCTURE OF AN ANTITUMOR CH2-DOMAIN-DELETED HUMANIZED ANTIBODY
2ajf STRUCTURE OF SARS CORONAVIRUS SPIKE RECEPTOR-BINDING DOMAIN COMPLEXED WITH ITS RECEPTOR
2dd8 STRUCTURE OF SARS CORONAVIRUS RECEPTOR-BINDING DOMAIN COMPLEXED WITH CROSS-REACTIVE NEUTRALIZING ANTIBODY