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(-) Description

Title :  CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLH COLLAGENASE COLLAGEN BINDING DOMAIN 3 AT 2.2 ANGSTROM RESOLUTION IN THE PRESENCE OF CALCIUM AND CADMIUM
 
Authors :  J. Sakon, S. T. L. Philominathan, R. Bauer, O. Matsushita
Date :  08 Sep 09  (Deposition) - 29 Sep 10  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Beta Barrel, Dual Calcium-Binding Motif, Collagen, Cell Adhesion (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 - COLH PROTEIN
    Chains: A, B, C
    EC Number: 3.4.24.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: COLLAGEN BINDING DOMAIN
    Gene: COLH
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498
    Synonym: COLLAGENASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CD9Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:870 , ASN A:872 , ASN A:873 , ASP A:897 , GLN A:898 , ASP A:899 , CD A:1002BINDING SITE FOR RESIDUE CA A 1001
02AC2SOFTWAREGLU A:868 , GLU A:870 , THR A:891 , ASP A:897 , ASP A:899 , CA A:1001BINDING SITE FOR RESIDUE CD A 1002
03AC3SOFTWAREGLU A:876 , HOH A:1136BINDING SITE FOR RESIDUE CD A 1003
04AC4SOFTWAREGLU A:930BINDING SITE FOR RESIDUE CD A 1004
05AC5SOFTWAREGLU B:870 , ASN B:872 , ASN B:873 , ASP B:897 , GLN B:898 , ASP B:899 , CD B:1002BINDING SITE FOR RESIDUE CA B 1001
06AC6SOFTWAREGLU B:868 , GLU B:870 , THR B:891 , ASP B:897 , ASP B:899 , CA B:1001 , HOH B:1104BINDING SITE FOR RESIDUE CD B 1002
07AC7SOFTWAREGLU B:876BINDING SITE FOR RESIDUE CD B 1003
08AC8SOFTWAREGLU B:930BINDING SITE FOR RESIDUE CD B 1004
09AC9SOFTWAREGLU C:870 , ASN C:872 , ASN C:873 , ASP C:897 , GLN C:898 , ASP C:899 , CD C:1002BINDING SITE FOR RESIDUE CA C 1001
10BC1SOFTWAREGLU C:868 , GLU C:870 , THR C:891 , ASP C:897 , ASP C:899 , CA C:1001 , HOH C:1119BINDING SITE FOR RESIDUE CD C 1002
11BC2SOFTWAREGLU C:876 , HOH C:1114 , HOH C:1144BINDING SITE FOR RESIDUE CD C 1003
12BC3SOFTWAREGLU C:930 , HOH C:1151BINDING SITE FOR RESIDUE CD C 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:870 -Pro A:871
2Gly A:880 -Pro A:881
3Glu B:870 -Pro B:871
4Gly B:880 -Pro B:881
5Glu C:870 -Pro C:871
6Gly C:880 -Pro C:881

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JQX)

(-) 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:117
 aligned with Q46085_HATHI | Q46085 from UniProtKB/TrEMBL  Length:1021

    Alignment length:117
                                   912       922       932       942       952       962       972       982       992      1002      1012       
        Q46085_HATHI    903 YPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGYGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSV 1019
               SCOP domains d3jqxa_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................eeeee......eeeeeee...eeeeeeeee....eeeeeee.....eeee.ee...eeeeeeee...eeeeeeeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                3jqx A  863 YPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGYGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSV  979
                                   872       882       892       902       912       922       932       942       952       962       972       


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with Q46085_HATHI | Q46085 from UniProtKB/TrEMBL  Length:1021

    Alignment length:120
                                   911       921       931       941       951       961       971       981       991      1001      1011      1021
        Q46085_HATHI    902 VYPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGYGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSVGR 1021
               SCOP domains d3jqxb_ B: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhh.........eeeee......eeeeeee...eeeeeeeee....eeeeeeee....eeee.ee...eeeeeeee...eeeeeeeeeee...eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                3jqx B  862 VYPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGYGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSVGR  981
                                   871       881       891       901       911       921       931       941       951       961       971       981


Chain C from PDB  Type:PROTEIN  Length:121
 aligned with Q46085_HATHI | Q46085 from UniProtKB/TrEMBL  Length:1021

    Alignment length:121
                                   910       920       930       940       950       960       970       980       990      1000      1010      1020 
        Q46085_HATHI    901 PVYPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGYGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSVGR 1021
               SCOP domains d3jqxc_ C: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh.........eeeee......eeeeeee...eeeeeeeee....eeeeeee.....eeee.ee...eeeeeeee...eeeeeeeeeee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                3jqx C  861 QVYPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGYGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSVGR  981
                                   870       880       890       900       910       920       930       940       950       960       970       980
   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  (1, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q46085_HATHI | Q46085)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  3jqx
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  3.4.24.3
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 Related Entries

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

UniProtKB/TrEMBL
        Q46085_HATHI | Q46085: 3jqw 4ar1 4arf 4jgu 4u6t 4u7k

(-) Related Entries Specified in the PDB File

1nqj SIMILAR TO COLLAGEN BINDING DOMAIN FROM CLOSTRIDIAL COLG COLLAGENASE
2o8o SIMILAR TO COLLAGEN BINDING DOMAIN FROM CLOSTRIDIAL COLG COLLAGENASE
3jqu COLG COLLAGENASE PKD DOMAIN AT 1.4A RESOLUTION
3jqw COLLAGEN BINDING DOMAIN 3 AT 2A IN PRESENCE OF CALCIUM