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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZN-RIDC1 COMPLEX STABILIZED BY BMOE CROSSLINKS
 
Authors :  E. N. Salgado, F. A. Tezcan
Date :  26 Feb 11  (Deposition) - 22 Jun 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Four-Helix Bundle, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. N. Salgado, J. D. Brodin, M. M. To, F. A. Tezcan
Templated Construction Of A Zn-Selective Protein Dimerization Motif.
Inorg. Chem. V. 50 6323 2011
PubMed-ID: 21648390  |  Reference-DOI: 10.1021/IC200746M

(-) Compounds

Molecule 1 - CYTOCHROME CB562
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ME72Ligand/Ion1,1'-ETHANE-1,2-DIYLBIS(1H-PYRROLE-2,5-DIONE)
3ZN13Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:4 , MET A:7 , ASN A:11 , LEU A:14 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , TYR A:105 , ARG A:106 , ZN A:108 , ASP C:5 , ARG D:106 , HEM D:150BINDING SITE FOR RESIDUE HEM A 150
02AC2SOFTWAREHIS A:73 , HIS A:77 , ASP C:74 , HIS D:63BINDING SITE FOR RESIDUE ZN A 500
03AC3SOFTWAREALA A:1 , ASP A:39 , ASP B:2 , ASP B:5BINDING SITE FOR RESIDUE ZN A 107
04AC4SOFTWAREGLU A:4 , ZN A:110 , HEM A:150 , ZN D:107 , HEM D:150BINDING SITE FOR RESIDUE ZN A 108
05AC5SOFTWAREASP A:2 , ASP A:5 , ZN B:107 , ZN B:108 , HEM B:150 , GLU C:4BINDING SITE FOR RESIDUE ZN A 109
06AC6SOFTWAREGLU A:4 , ZN A:108 , ASP C:2 , ASP C:5 , ZN D:107BINDING SITE FOR RESIDUE ZN A 110
07AC7SOFTWAREASP A:2 , ZN A:109 , GLU B:4 , MET B:7 , GLU B:8 , ASN B:11 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ZN B:107 , ZN B:108 , HOH B:111 , HEM C:150BINDING SITE FOR RESIDUE HEM B 150
08AC8SOFTWAREHIS B:73 , HIS B:77 , HIS C:63 , ASP D:74BINDING SITE FOR RESIDUE ZN B 500
09AC9SOFTWAREASP A:5 , ZN A:109 , GLU B:4 , ZN B:108 , HEM B:150BINDING SITE FOR RESIDUE ZN B 107
10BC1SOFTWAREASP A:5 , ZN A:109 , ZN B:107 , HEM B:150 , GLU C:4 , HEM C:150BINDING SITE FOR RESIDUE ZN B 108
11BC2SOFTWARECYS A:82 , GLU C:81 , CYS C:82BINDING SITE FOR RESIDUE ME7 C 501
12BC3SOFTWAREASP A:74 , HIS B:63 , HIS C:73 , HIS C:77BINDING SITE FOR RESIDUE ZN C 500
13BC4SOFTWAREGLU B:4 , ZN B:108 , HEM B:150 , GLU C:4 , MET C:7 , ASN C:11 , LEU C:14 , PRO C:45 , PRO C:46 , PHE C:61 , GLY C:64 , CYS C:98 , CYS C:101 , HIS C:102 , ARG C:106BINDING SITE FOR RESIDUE HEM C 150
14BC5SOFTWAREALA C:1 , ASP C:39 , ASP D:2 , ASP D:5BINDING SITE FOR RESIDUE ZN C 107
15BC6SOFTWAREGLU A:8 , ASP A:12 , GLU C:8 , ASP C:12BINDING SITE FOR RESIDUE ZN C 108
16BC7SOFTWAREHIS A:63 , ASP B:74 , HIS D:73 , HIS D:77BINDING SITE FOR RESIDUE ZN D 500
17BC8SOFTWAREGLU B:81 , CYS B:82 , GLU D:49 , ASP D:50 , SER D:52 , ASN D:80 , GLU D:81 , CYS D:82BINDING SITE FOR RESIDUE ME7 D 501
18BC9SOFTWAREZN A:108 , HEM A:150 , LEU D:3 , GLU D:4 , MET D:7 , ASN D:11 , PRO D:45 , PRO D:46 , PHE D:61 , PHE D:65 , CYS D:98 , CYS D:101 , HIS D:102 , ARG D:106 , ZN D:107BINDING SITE FOR RESIDUE HEM D 150
19CC1SOFTWAREZN A:108 , ZN A:110 , ASP C:5 , GLU D:4 , HEM D:150BINDING SITE FOR RESIDUE ZN D 107

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QVY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QVY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QVY)

(-) Sequences/Alignments

Asymmetric/Biological 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:106
                                                                                                                                          
               SCOP domains d3qvya_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3qvy A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANECKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d3qvyb_ B: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3qvy B   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANECKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d3qvyc_ C: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3qvy C   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANECKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain D from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d3qvyd_ D: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3qvy D   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANECKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
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    → 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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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(-) Related Entries Specified in the PDB File

3hni 3iq6 3qvz 3qw0 3qw1