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(-) Description

Title :  CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE COLLAGEN-BINDING DOMAIN 3B AT 1.35 ANGSTROM RESOLUTION IN PRESENCE OF CALCIUM NITRATE
 
Authors :  S. T. L. Philominathan, J. J. Wilson, R. Bauer, O. Matsushita, J. Sakon
Date :  24 Oct 12  (Deposition) - 12 Dec 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Sandwich Jelly-Roll, Collagen Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Bauer, J. J. Wilson, S. T. Philominathan, D. Davis, O. Matsushita, J. Sakon
Structural Comparison Of Colh And Colg Collagen-Binding Domains From Clostridium Histolyticum.
J. Bacteriol. V. 195 318 2013
PubMed-ID: 23144249  |  Reference-DOI: 10.1128/JB.00010-12

(-) Compounds

Molecule 1 - COLLAGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1006-1118
    Gene: COLG
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498
 
Molecule 2 - COLLAGENASE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 999-1118
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3NO31Ligand/IonNITRATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:901 , ASN A:903 , ASP A:904 , ASP A:927 , ARG A:929 , ASP A:930BINDING SITE FOR RESIDUE CA A 1101
2AC2SOFTWAREGLU A:899 , GLU A:901 , SER A:922 , ASP A:927 , ASP A:930 , HOH A:1205BINDING SITE FOR RESIDUE CA A 1102
3AC3SOFTWARELYS A:937 , GLU A:938 , LYS A:1008BINDING SITE FOR RESIDUE CL A 1103
4AC4SOFTWARELEU A:958 , PRO A:960 , ARG A:967 , ILE A:968 , THR A:969 , TYR A:989BINDING SITE FOR RESIDUE NO3 A 1104
5AC5SOFTWAREGLU B:901 , ASN B:903 , ASP B:904 , ASP B:927 , ARG B:929 , ASP B:930BINDING SITE FOR RESIDUE CA B 1101
6AC6SOFTWAREGLU B:899 , GLU B:901 , SER B:922 , ASP B:927 , ASP B:930 , HOH B:1204BINDING SITE FOR RESIDUE CA B 1102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HPK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:901 -Asn A:902
2Glu B:901 -Asn B:902

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HPK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HPK)

(-) Exons   (0, 0)

(no "Exon" information available for 4HPK)

(-) 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:110
                                                                                                                                               
               SCOP domains d4hpka_ A: Class 1 collagenase                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......hhhhhee.......eeeee.....eeeeeeee...eeeeeeeee....eeeeeeee.....ee.eee..eeeeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                4hpk A  896 KLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1008
                                   905       915       925       935       945       955      |968       978       988       998      1008
                                                                                            962|                                          
                                                                                             966                                          


Chain B from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d4hpkb_ B: Class 1 collagenase                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......hhhhhee.....eeeeeee.....eeeeeeee...eeeeeeeee....eeeeeeee...ee.eee..eeeeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                4hpk B  891 IPGNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1008
                                   900       910       920       930       940       950       960 ||    975       985       995      1005   
                                                                                                 962|                                        
                                                                                                  968
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HPK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HPK)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9X721_HATHI | Q9X721: 2o8o
UniProtKB/TrEMBL
        Q9X721_HATHI | Q9X721: 2y3u 2y50 2y6i 2y72 4aqo 4are 4jrw 4tn9 5iku

(-) Related Entries Specified in the PDB File

1nqd A BACTERIAL COLLAGEN-BINDING DOMAIN WITH NOVEL CALCIUM- BINDING MOTIF
1nqj SAME PROTEIN IN THE ABSENCE OF CALCIUM
2o8o SAME PROTEIN REFINED USING SHELX97
3jqw COLH COLLAGENASE COLLAGEN BINDING DOMAIN 3 IN THE PRESENCE OF CALCIUM
3jqx COLH COLLAGENASE COLLAGEN BINDING DOMAIN 3 IN THE PRESENCE OF CALCIUM AND CADMIUM