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

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE METALLO-BETA-LACTAMASE (TM0894) FROM THERMOTOGA MARITIMA AT 2.10 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  26 May 05  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Tm0894) From Thermotoga Maritima At 2. 10 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TM0894
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0894
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric/Biological Unit (4, 26)
No.NameCountTypeFull Name
1MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NI8Ligand/IonNICKEL (II) ION
4PO45Ligand/IonPHOSPHATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:73 , HIS A:74 , ASP A:162 , HIS A:199 , NI A:302 , HOH A:387 , HOH A:425BINDING SITE FOR RESIDUE NI A 301
02AC2SOFTWAREHIS A:69 , HIS A:71 , HIS A:140 , ASP A:162 , NI A:301 , HOH A:306 , HOH A:425BINDING SITE FOR RESIDUE NI A 302
03AC3SOFTWAREASP B:73 , HIS B:74 , ASP B:162 , HIS B:199 , NI B:302 , HOH B:336 , HOH B:402BINDING SITE FOR RESIDUE NI B 301
04AC4SOFTWAREHIS B:69 , HIS B:71 , HIS B:140 , ASP B:162 , NI B:301 , HOH B:305 , HOH B:402BINDING SITE FOR RESIDUE NI B 302
05AC5SOFTWAREASP C:73 , HIS C:74 , ASP C:162 , HIS C:199 , NI C:302 , HOH C:361 , HOH C:393BINDING SITE FOR RESIDUE NI C 301
06AC6SOFTWAREHIS C:69 , HIS C:71 , HIS C:140 , ASP C:162 , NI C:301 , HOH C:305 , HOH C:393BINDING SITE FOR RESIDUE NI C 302
07AC7SOFTWAREASP D:73 , HIS D:74 , ASP D:162 , HIS D:199 , NI D:302 , HOH D:399 , HOH D:409BINDING SITE FOR RESIDUE NI D 301
08AC8SOFTWAREHIS D:69 , HIS D:71 , HIS D:140 , ASP D:162 , NI D:301 , HOH D:306 , HOH D:399BINDING SITE FOR RESIDUE NI D 302
09AC9SOFTWARELYS A:95 , ALA A:141 , ARG A:142 , HOH A:407 , HOH A:433 , LYS D:175BINDING SITE FOR RESIDUE PO4 A 303
10BC1SOFTWARELYS B:95 , ALA B:141 , ARG B:142 , LYS C:175BINDING SITE FOR RESIDUE PO4 B 303
11BC2SOFTWARELYS B:175 , LYS C:95 , ALA C:141 , ARG C:142BINDING SITE FOR RESIDUE PO4 C 303
12BC3SOFTWARELYS A:175 , LYS D:95 , ALA D:141 , ARG D:142 , HOH D:343 , HOH D:367BINDING SITE FOR RESIDUE PO4 D 304
13BC4SOFTWARESER D:126 , GLU D:130 , LYS D:131 , LEU D:148 , ARG D:156 , HOH D:372BINDING SITE FOR RESIDUE MPD D 305
14BC5SOFTWARESER B:126 , GLU B:130 , LEU B:148 , ASP B:150 , ARG B:156 , GLU D:130BINDING SITE FOR RESIDUE MPD B 304
15BC6SOFTWAREPHE A:135 , ARG A:156 , ARG A:188 , VAL A:189 , ASP C:60 , ASP C:61 , ASN C:83BINDING SITE FOR RESIDUE MPD A 304
16BC7SOFTWAREARG C:33 , TYR C:87 , LEU C:127 , PHE C:128BINDING SITE FOR RESIDUE MPD C 304
17BC8SOFTWAREARG A:33 , PHE A:128BINDING SITE FOR RESIDUE MPD A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZTC)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZTC)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZTC)

(-) 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:209
 aligned with Q9WZZ6_THEMA | Q9WZZ6 from UniProtKB/TrEMBL  Length:209

    Alignment length:209
                              1                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         
         Q9WZZ6_THEMA     - --MELKILVTGGNVFVPGRLNAHFSTVVYLEHKDRRIIIDPGNLSSMDELEEKFSELGISPDDITDVLFTHVHLDHIFNSVLFENATFYVHEVYKTKNYLSFGTIVGRIYSKVISSWKNVVLLKGEESLFDEKVKVFHTPWHAREHLSFLLDTENAGRVLITGDITPNRLSYYDIIKGYGSVQVKNFLDRVGRIDLLVFPHDAPLKPEV 207
               SCOP domains --d1ztca1 A:1-207 Hypothetical protein TM0894                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeee...ee.....eeeeee..eeeee...hhhhhhhhhhhhhhhh.hhhhh.eee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eeee....ee....eeeee........eeeeeee...eeeee.hhhh.hhhhhhhhhh...hhhhhhhhhhhh...eee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ztc A  -1 HHmELKILVTGGNVFVPGRLNAHFSTVVYLEHKDRRIIIDPGNLSSmDELEEKFSELGISPDDITDVLFTHVHLDHIFNSVLFENATFYVHEVYKTKNYLSFGTIVGRIYSKVISSWKNVVLLKGEESLFDEKVKVFHTPWHAREHLSFLLDTENAGRVLITGDITPNRLSYYDIIKGYGSVQVKNFLDRVGRIDLLVFPHDAPLKPEV 207
                              |      8        18        28        38      | 48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         
                              |                                          45-MSE                                                                                                                                                              
                              1-MSE                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with Q9WZZ6_THEMA | Q9WZZ6 from UniProtKB/TrEMBL  Length:209

    Alignment length:209
                              1                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         
         Q9WZZ6_THEMA     - --MELKILVTGGNVFVPGRLNAHFSTVVYLEHKDRRIIIDPGNLSSMDELEEKFSELGISPDDITDVLFTHVHLDHIFNSVLFENATFYVHEVYKTKNYLSFGTIVGRIYSKVISSWKNVVLLKGEESLFDEKVKVFHTPWHAREHLSFLLDTENAGRVLITGDITPNRLSYYDIIKGYGSVQVKNFLDRVGRIDLLVFPHDAPLKPEV 207
               SCOP domains d1ztcb_ B: Hypothetical protein TM0894                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeee...ee.....eeeeee..eeeee...hhhhhhhhhhhhhhhh.hhhhh.eee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeee....ee....eeeee........eeeeeee...eeeee.hhhh.hhhhhhhhhh...hhhhhhhhhhhh...eee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ztc B  -1 HHmELKILVTGGNVFVPGRLNAHFSTVVYLEHKDRRIIIDPGNLSSmDELEEKFSELGISPDDITDVLFTHVHLDHIFNSVLFENATFYVHEVYKTKNYLSFGTIVGRIYSKVISSWKNVVLLKGEESLFDEKVKVFHTPWHAREHLSFLLDTENAGRVLITGDITPNRLSYYDIIKGYGSVQVKNFLDRVGRIDLLVFPHDAPLKPEV 207
                              |      8        18        28        38      | 48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         
                              1-MSE                                      45-MSE                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:207
 aligned with Q9WZZ6_THEMA | Q9WZZ6 from UniProtKB/TrEMBL  Length:209

    Alignment length:207
                              1                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       
         Q9WZZ6_THEMA     - --MELKILVTGGNVFVPGRLNAHFSTVVYLEHKDRRIIIDPGNLSSMDELEEKFSELGISPDDITDVLFTHVHLDHIFNSVLFENATFYVHEVYKTKNYLSFGTIVGRIYSKVISSWKNVVLLKGEESLFDEKVKVFHTPWHAREHLSFLLDTENAGRVLITGDITPNRLSYYDIIKGYGSVQVKNFLDRVGRIDLLVFPHDAPLKP 205
               SCOP domains d1ztcc_ C: Hypothetical protein TM0894                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeee...ee.....eeeeee..eeeee...hhhhhhhhhhhhhhhh.hhhhh.eee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eeee....ee....eeeee........eeeeeee...eeeee.hhhh.hhhhhhhhhh...hhhhhhhhhhhh...eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ztc C  -1 HHmELKILVTGGNVFVPGRLNAHFSTVVYLEHKDRRIIIDPGNLSSmDELEEKFSELGISPDDITDVLFTHVHLDHIFNSVLFENATFYVHEVYKTKNYLSFGTIVGRIYSKVISSWKNVVLLKGEESLFDEKVKVFHTPWHAREHLSFLLDTENAGRVLITGDITPNRLSYYDIIKGYGSVQVKNFLDRVGRIDLLVFPHDAPLKP 205
                              |      8        18        28        38      | 48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       
                              1-MSE                                      45-MSE                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:208
 aligned with Q9WZZ6_THEMA | Q9WZZ6 from UniProtKB/TrEMBL  Length:209

    Alignment length:208
                              1                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198        
         Q9WZZ6_THEMA     - --MELKILVTGGNVFVPGRLNAHFSTVVYLEHKDRRIIIDPGNLSSMDELEEKFSELGISPDDITDVLFTHVHLDHIFNSVLFENATFYVHEVYKTKNYLSFGTIVGRIYSKVISSWKNVVLLKGEESLFDEKVKVFHTPWHAREHLSFLLDTENAGRVLITGDITPNRLSYYDIIKGYGSVQVKNFLDRVGRIDLLVFPHDAPLKPE 206
               SCOP domains d1ztcd_ D: Hypothetical protein TM0894                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeee...ee.....eeeeee..eeeee...hhhhhhhhhhhhhhhh.hhhhh.eee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeee....ee....eeeee........eeeeeee...eeeee.hhhh.hhhhhhhhhh...hhhhhhhhhhhh...eee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ztc D  -1 HHmELKILVTGGNVFVPGRLNAHFSTVVYLEHKDRRIIIDPGNLSSmDELEEKFSELGISPDDITDVLFTHVHLDHIFNSVLFENATFYVHEVYKTKNYLSFGTIVGRIYSKVISSWKNVVLLKGEESLFDEKVKVFHTPWHAREHLSFLLDTENAGRVLITGDITPNRLSYYDIIKGYGSVQVKNFLDRVGRIDLLVFPHDAPLKPE 206
                              |      8        18        28        38      | 48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198        
                              1-MSE                                      45-MSE
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZTC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1ZTC)

 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
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ztc)
 

(-) 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
  1ztc
    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
  Q9WZZ6_THEMA | Q9WZZ6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q9WZZ6_THEMA | Q9WZZ6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1ZTC)

(-) Related Entries Specified in the PDB File

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