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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-IL-13 ANTIBODY C836
 
Authors :  A. Teplyakov, G. Obmolova, T. Malia, G. L. Gilliland
Date :  28 Dec 09  (Deposition) - 10 Nov 10  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Immunoglobulin Fold, Monoclonal Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Teplyakov, G. Obmolova, T. J. Malia, G. Gilliland
Antigen Recognition By Antibody C836 Through Adjustment Of Vl/Vh Packing
Acta Crystallogr. , Sect. F V. 67 1165 2011
PubMed: search

(-) Compounds

Molecule 1 - C836 LIGHT CHAIN
    Chains: L, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090,9606
 
Molecule 2 - C836 HEAVY CHAIN
    Chains: H, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: FD FRAGMENT OF THE HEAVY CHAIN, CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090,9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN L:6 , SER L:7 , PRO L:8 , SER L:9 , SER L:14 , GLU L:17 , LYS L:107BINDING SITE FOR RESIDUE SO4 L 1001
2AC2SOFTWAREPHE H:174 , PRO H:175 , SER H:185 , LEU H:186 , SER H:187 , GLN L:160 , SER L:162 , SER L:176 , SER L:177 , THR L:178BINDING SITE FOR RESIDUE GOL L 1005
3AC3SOFTWAREASP B:74 , THR B:75 , SER B:76 , ASP H:57 , LYS H:59 , ILE H:71 , SER H:72 , LYS H:73BINDING SITE FOR RESIDUE SO4 H 1002
4AC4SOFTWARETRP H:54 , ASP H:56 , ASP H:103 , TYR H:104BINDING SITE FOR RESIDUE ACT H 1004
5AC5SOFTWAREASN B:163 , ALA B:166 , GLN B:200BINDING SITE FOR RESIDUE ACT B 1003

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:97
4B:148 -B:204
5H:22 -H:97
6H:148 -H:204
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:154 -Pro H:155
5Glu H:156 -Pro H:157
6Ser A:7 -Pro A:8
7Tyr A:94 -Pro A:95
8Tyr A:140 -Pro A:141
9Phe B:154 -Pro B:155
10Glu B:156 -Pro B:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L7E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L7E)

(-) Exons   (0, 0)

(no "Exon" information available for 3L7E)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains d3l7ea1 A:1-107 automated matches                                                                          d3l7ea2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l7e A   1 DVQITQSPSYLAASPGETITLNCRASKSISKYLAWYQEKPGKTNKLLIYSGSTLQSGIPSRFSGSGSGTDFTLTISSLEPEDFAMYFCQQHNEYPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeeee.....eeeeeee....eee...hhh.eeeee.....eeeeee...hhhh.eeeeeeee.......eeee...eeeee........eeeee....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l7e B   1 QVTLKESGPGILQPSQTLSLTCSFSGFSLSTYGMGVGWIRQPSGKGLEWLAHIWWDDVKRYNPALKSRLTISKDTSGSQVFLKIASVDTSDTATYYCARMGSDYDVWFDYWGQGTLVTVSAASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 146       156       166       176       186       196       206       216     
                                                                                                                                                                135|                                                                               
                                                                                                                                                                 142                                                                               


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee....eee.......eeeee.....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh...eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l7e H   1 QVTLKESGPGILQPSQTLSLTCSFSGFSLSTYGMGVGWIRQPSGKGLEWLAHIWWDDVKRYNPALKSRLTISKDTSGSQVFLKIASVDTSDTATYYCARMGSDYDVWFDYWGQGTLVTVSAASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||145       155       165       175       185       195       205       215      
                                                                                                                                                                 136|                                                                               
                                                                                                                                                                  142                                                                               


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3l7el1 L:1-107 automated matches                                                                          d3l7el2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l7e L   1 DVQITQSPSYLAASPGETITLNCRASKSISKYLAWYQEKPGKTNKLLIYSGSTLQSGIPSRFSGSGSGTDFTLTISSLEPEDFAMYFCQQHNEYPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L7E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3L7E)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3L7E)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3l5w IL-13:C836 FAB COMPLEX
3l5x IL-13:H2L6 FAB COMPLEX
3l5y IL-13:M1295 FAB COMPLEX
3l7f