Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Kanagawa, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  01 Jun 05  (Deposition) - 01 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Beta Alpha Beta Motif, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kanagawa, S. Yokoyama, S. Kuramitsu
Crystal Structure Of A Hypothetical Protein From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TTHA0625
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2CV9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CV9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CV9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CV9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CV9)

(-) Exons   (0, 0)

(no "Exon" information available for 2CV9)

(-) 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:252
 aligned with Q5SKL8_THET8 | Q5SKL8 from UniProtKB/TrEMBL  Length:252

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
         Q5SKL8_THET8     1 MRVLFIGDVMAEPGLRAVGLHLPDIRDRYDLVIANGENAARGKGLDRRSYRLLREAGVDLVSLGNHAWDHKEVYALLESEPVVRPLNYPPGTPGKGFWRLEVGGESLLFVQVMGRIFMDPLDDPFRALDRLLEEEKADYVLVEVHAEATSEKMALAHYLDGRASAVLGTHTHVPTLDATRLPKGTLYQTDVGMTGTYHSIIGGEVETFLARFLTGRPQPFRAAQGKARFHATELVFEGGRPVAISPYVWEEP 252
               SCOP domains d2cv9a1 A:1-252 Hypothetical protein TTHA0625                                                                                                                                                                                                                SCOP domains
               CATH domains -2cv9A00 A:2-252 Phosphatase                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhh..eee.........hhhhhhhhh.ee.............eeeeee..eeeeeeeee.........hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh....eeeee.........ee.....eee...............hhhhhhhhhhhh............eeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cv9 A   1 mRVLFIGDVmAEPGLRAVGLHLPDIRDRYDLVIANGENAARGKGLDRRSYRLLREAGVDLVSLGNHAWDHKEVYALLESEPVVRPLNYPPGTPGKGFWRLEVGGESLLFVQVmGRIFmDPLDDPFRALDRLLEEEKADYVLVEVHAEATSEKmALAHYLDGRASAVLGTHTHVPTLDATRLPKGTLYQTDVGmTGTYHSIIGGEVETFLARFLTGRPQPFRAAQGKARFHATELVFEGGRPVAISPYVWEEP 252
                            |       10        20        30        40        50        60        70        80        90       100       110  |    120       130       140       150  |    160       170       180       190  |    200       210       220       230       240       250  
                            |       10-MSE                                                                                                113-MSE|                                153-MSE                                 193-MSE                                                       
                            1-MSE                                                                                                              118-MSE                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with Q5SKL8_THET8 | Q5SKL8 from UniProtKB/TrEMBL  Length:252

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
         Q5SKL8_THET8     1 MRVLFIGDVMAEPGLRAVGLHLPDIRDRYDLVIANGENAARGKGLDRRSYRLLREAGVDLVSLGNHAWDHKEVYALLESEPVVRPLNYPPGTPGKGFWRLEVGGESLLFVQVMGRIFMDPLDDPFRALDRLLEEEKADYVLVEVHAEATSEKMALAHYLDGRASAVLGTHTHVPTLDATRLPKGTLYQTDVGMTGTYHSIIGGEVETFLARFLTGRPQPFRAAQGKARFHATELVFEGGRPVAISPYVWEEP 252
               SCOP domains d2cv9b_ B: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains -2cv9B00 B:2-252 Phosphatase                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhh..eee.........hhhhhhhhh.ee.............eeeeee..eeeeeeeee.........hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh....eeeee.........ee.....eee...............hhhhhhhhhhhh............eeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cv9 B   1 mRVLFIGDVmAEPGLRAVGLHLPDIRDRYDLVIANGENAARGKGLDRRSYRLLREAGVDLVSLGNHAWDHKEVYALLESEPVVRPLNYPPGTPGKGFWRLEVGGESLLFVQVmGRIFmDPLDDPFRALDRLLEEEKADYVLVEVHAEATSEKmALAHYLDGRASAVLGTHTHVPTLDATRLPKGTLYQTDVGmTGTYHSIIGGEVETFLARFLTGRPQPFRAAQGKARFHATELVFEGGRPVAISPYVWEEP 252
                            |       10        20        30        40        50        60        70        80        90       100       110  |    120       130       140       150  |    160       170       180       190  |    200       210       220       230       240       250  
                            1-MSE   10-MSE                                                                                                113-MSE|                                153-MSE                                 193-MSE                                                       
                                                                                                                                               118-MSE                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with Q5SKL8_THET8 | Q5SKL8 from UniProtKB/TrEMBL  Length:252

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
         Q5SKL8_THET8     1 MRVLFIGDVMAEPGLRAVGLHLPDIRDRYDLVIANGENAARGKGLDRRSYRLLREAGVDLVSLGNHAWDHKEVYALLESEPVVRPLNYPPGTPGKGFWRLEVGGESLLFVQVMGRIFMDPLDDPFRALDRLLEEEKADYVLVEVHAEATSEKMALAHYLDGRASAVLGTHTHVPTLDATRLPKGTLYQTDVGMTGTYHSIIGGEVETFLARFLTGRPQPFRAAQGKARFHATELVFEGGRPVAISPYVWEEP 252
               SCOP domains d2cv9c_ C: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains -2cv9C00 C:2-252 Phosphatase                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhh..eee...hhhhhhhhhhhhhhh.ee.............eeeeee..eeeeeeeee.........hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh....eeeee.........ee.....eee...............hhhhhhhhhhhh............eeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cv9 C   1 mRVLFIGDVmAEPGLRAVGLHLPDIRDRYDLVIANGENAARGKGLDRRSYRLLREAGVDLVSLGNHAWDHKEVYALLESEPVVRPLNYPPGTPGKGFWRLEVGGESLLFVQVmGRIFmDPLDDPFRALDRLLEEEKADYVLVEVHAEATSEKmALAHYLDGRASAVLGTHTHVPTLDATRLPKGTLYQTDVGmTGTYHSIIGGEVETFLARFLTGRPQPFRAAQGKARFHATELVFEGGRPVAISPYVWEEP 252
                            |       10        20        30        40        50        60        70        80        90       100       110  |    120       130       140       150  |    160       170       180       190  |    200       210       220       230       240       250  
                            1-MSE   10-MSE                                                                                                113-MSE|                                153-MSE                                 193-MSE                                                       
                                                                                                                                               118-MSE                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:252
 aligned with Q5SKL8_THET8 | Q5SKL8 from UniProtKB/TrEMBL  Length:252

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
         Q5SKL8_THET8     1 MRVLFIGDVMAEPGLRAVGLHLPDIRDRYDLVIANGENAARGKGLDRRSYRLLREAGVDLVSLGNHAWDHKEVYALLESEPVVRPLNYPPGTPGKGFWRLEVGGESLLFVQVMGRIFMDPLDDPFRALDRLLEEEKADYVLVEVHAEATSEKMALAHYLDGRASAVLGTHTHVPTLDATRLPKGTLYQTDVGMTGTYHSIIGGEVETFLARFLTGRPQPFRAAQGKARFHATELVFEGGRPVAISPYVWEEP 252
               SCOP domains d2cv9d_ D: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains -2cv9D00 D:2-252 Phosphatase                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh.ee.............eeeeee..eeeeeeeee.........hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh.....eeeee.........ee.....eee...............hhhhhhhhhhhh............eeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cv9 D   1 mRVLFIGDVmAEPGLRAVGLHLPDIRDRYDLVIANGENAARGKGLDRRSYRLLREAGVDLVSLGNHAWDHKEVYALLESEPVVRPLNYPPGTPGKGFWRLEVGGESLLFVQVmGRIFmDPLDDPFRALDRLLEEEKADYVLVEVHAEATSEKmALAHYLDGRASAVLGTHTHVPTLDATRLPKGTLYQTDVGmTGTYHSIIGGEVETFLARFLTGRPQPFRAAQGKARFHATELVFEGGRPVAISPYVWEEP 252
                            |       10        20        30        40        50        60        70        80        90       100       110  |    120       130       140       150  |    160       170       180       190  |    200       210       220       230       240       250  
                            1-MSE   10-MSE                                                                                                113-MSE|                                153-MSE                                 193-MSE                                                       
                                                                                                                                               118-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  (2, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CV9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2CV9)

 Visualization

(-) Interactive Views

Asymmetric 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2cv9)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cv9)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  2cv9
    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
  Q5SKL8_THET8 | Q5SKL8
    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
  Q5SKL8_THET8 | Q5SKL8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5SKL8_THET8 | Q5SKL8: 2z06

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CV9)