Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  METALLOPROTEASE
 
Authors :  I. Botos, L. Scapozza, D. Zhang, L. A. Liotta, E. F. Meyer
Date :  12 Feb 96  (Deposition) - 12 Feb 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Metalloprotease, Zinc, Venom (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Botos, L. Scapozza, D. Zhang, L. A. Liotta, E. F. Meyer
Batimastat, A Potent Matrix Mealloproteinase Inhibitor, Exhibits An Unexpected Mode Of Binding.
Proc. Natl. Acad. Sci. Usa V. 93 2749 1996
PubMed-ID: 8610113  |  Reference-DOI: 10.1073/PNAS.93.7.2749
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATROLYSIN C
    Chains: A, B
    EC Number: 3.4.24.42
    Organism Common: WESTERN DIAMONDBACK RATTLESNAKE
    Organism Scientific: CROTALUS ATROX
    Organism Taxid: 8730
    Secretion: VENOM
    Synonym: BB-94, BATIMASTAT, HEMORRHAGIC TOXIN C, FORM D

 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
1BAT2Ligand/Ion4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE
2CA2Ligand/IonCALCIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:142 , HIS A:146 , HIS A:152 , BAT A:972BINDING SITE FOR RESIDUE ZN A 901
02AC2SOFTWAREGLU A:9 , ASP A:93 , CYS A:197 , ASN A:200BINDING SITE FOR RESIDUE CA A 903
03AC3SOFTWAREHIS B:142 , HIS B:146 , HIS B:152 , BAT B:973BINDING SITE FOR RESIDUE ZN B 902
04AC4SOFTWAREGLU B:9 , ASP B:93 , CYS B:197 , ASN B:200BINDING SITE FOR RESIDUE CA B 904
05AC5SOFTWAREGLU A:105 , GLU A:106 , LEU A:108 , GLY A:109 , LEU A:110 , THR A:139 , HIS A:142 , GLU A:143 , HIS A:146 , HIS A:152 , CYS A:164 , ILE A:165 , ARG A:167 , PRO A:168 , GLY A:169 , LEU A:170 , TYR A:176 , ZN A:901BINDING SITE FOR RESIDUE BAT A 972
06AC6SOFTWAREGLU B:106 , LEU B:108 , GLY B:109 , VAL B:138 , THR B:139 , HIS B:142 , GLU B:143 , HIS B:152 , CYS B:164 , ILE B:165 , ARG B:167 , PRO B:168 , GLY B:169 , LEU B:170 , THR B:171 , TYR B:176 , ZN B:902BINDING SITE FOR RESIDUE BAT B 973
07CAAUNKNOWNGLU A:9 , ASP A:93 , ASN A:200CALCIUM ION BINDING SITE
08CABUNKNOWNGLU B:9 , ASP B:93 , ASN B:200CALCIUM ION BINDING SITE
09ZNAUNKNOWNHIS A:142 , HIS A:146 , HIS A:152ZINC BINDING SITE
10ZNBUNKNOWNHIS B:142 , HIS B:146 , HIS B:152ZINC BINDING SITE

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:117 -A:197
2A:157 -A:164
3B:117 -B:197
4B:157 -B:164

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DTH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DTH)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADAM_MEPROPS50215 ADAM type metalloprotease domain profile.VM1AD_CROAT197-393
 		  2A:6-202
B:6-202
2ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.VM1AD_CROAT330-339
 		  2A:139-148
B:139-148

(-) Exons   (0, 0)

(no "Exon" information available for 1DTH)

(-) 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:202
 aligned with VM1AD_CROAT | P15167 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:202
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391  
          VM1AD_CROAT   192 QNLPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP 393
               SCOP domains d1dtha_ A: Snake venom metalloprotease                                                                                                                                                                     SCOP domains
               CATH domains 1dthA00 A:1-202 Collagenase (Catalytic Domain)                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee............hhhhhhhhhhhhhh.hhh.....eeeeee.........eee...........eeeee.....hhhhhhhhhhhhhhh................................hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----ADAM_MEPRO  PDB: A:6-202 UniProt: 197-393                                                                                                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dth A   1 QNLPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain B from PDB  Type:PROTEIN  Length:202
 aligned with VM1AD_CROAT | P15167 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:202
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391  
          VM1AD_CROAT   192 QNLPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP 393
               SCOP domains d1dthb_ B: Snake venom metalloprotease                                                                                                                                                                     SCOP domains
               CATH domains 1dthB00 B:1-202 Collagenase (Catalytic Domain)                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhh.hhh.eeeeeeeeee............hhhhhhhhhhhhhh.hhhh....eeeeee.......................eeeee.....hhhhhhhhhhhhhhh................................hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----ADAM_MEPRO  PDB: B:6-202 UniProt: 197-393                                                                                                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dth B   1 QNLPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DTH)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VM1AD_CROAT | P15167)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BAT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    CAA  [ RasMol ]  +environment [ RasMol ]
    CAB  [ RasMol ]  +environment [ RasMol ]
    ZNA  [ RasMol ]  +environment [ RasMol ]
    ZNB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dth)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1dth
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  VM1AD_CROAT | P15167
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.42
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  VM1AD_CROAT | P15167
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VM1AD_CROAT | P15167: 1atl 1htd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DTH)