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 :  CRYSTAL STRUCTURE OF PUTATIVE RIBOKINASE (10640157) FROM THERMOPLASMA ACIDOPHILUM AT 1.91 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Nov 07  (Deposition) - 04 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B
Keywords :  10640157, Putative Ribokinase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Ribokinase (10640157) From Thermoplasma Acidophilum At 1. 91 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOKINASE RELATED PROTEIN
    Atcc: 25905
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 10640157, TA0880
    Mutation: YES
    Organism Scientific: THERMOPLASMA ACIDOPHILUM DSM 1728
    Organism Taxid: 273075
    Strain: DSM 1728, AMRC-C165, IFO 15155, JCM 9062

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric/Biological Unit (3, 34)
No.NameCountTypeFull Name
1MSE26Mod. Amino AcidSELENOMETHIONINE
2PGO7Ligand/IonS-1,2-PROPANEDIOL
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:241 , SER A:242 , LYS A:245 , ARG B:241 , SER B:242 , LYS B:245 , HOH B:358BINDING SITE FOR RESIDUE PO4 B 288
2AC2SOFTWAREGLN A:108 , MSE A:111 , ALA A:112 , GLY A:130 , GLU A:151 , LYS A:154BINDING SITE FOR RESIDUE PGO A 288
3AC3SOFTWARETHR B:64 , SER B:89 , HOH B:301BINDING SITE FOR RESIDUE PGO B 289
4AC4SOFTWAREMSE B:62 , GLU B:73 , ASP B:271 , ARG B:274BINDING SITE FOR RESIDUE PGO B 290
5AC5SOFTWAREGLN A:150 , ASN A:173 , HIS A:175 , GLU A:176BINDING SITE FOR RESIDUE PGO A 289
6AC6SOFTWAREPRO B:189 , MSE B:206 , ASP B:207 , GLY B:208 , HOH B:355BINDING SITE FOR RESIDUE PGO B 291
7AC7SOFTWARETHR A:196 , GLY A:198 , GLY A:201 , PHE A:229 , HOH A:295 , HOH A:406BINDING SITE FOR RESIDUE PGO A 290
8AC8SOFTWARETYR B:168 , THR B:192 , MSE B:206 , ILE B:243 , HOH B:356BINDING SITE FOR RESIDUE PGO B 292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BF5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:90 -Pro A:91
2Gly B:90 -Pro B:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BF5)

(-) Exons   (0, 0)

(no "Exon" information available for 3BF5)

(-) 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:284
 aligned with NK_THEAC | Q9HJT3 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:284
                             1                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279    
             NK_THEAC     - -MRFLAYFGHLNIDVLISVDSIPREGSVNVKDLRPRFGGTAGNFAIVAQKFRIPFDLYSAVGMKTHREYLAMIESMGINTGHVEKFEDESGPICYIATDGKKQVSFMHQGAMEKWKPQLADEYEYVHFSTGPNYLDMAKSIRSKIIFDPSQEIHKYSKDELKKFHEISYMSIFNDHEYRVFREMTGLSSPKVTTIVTNGERGSSLFMDGKKYDFPAIPSSGDTVGAGDSFRAGLYLALYNRRSIEKGMIYGTIIAHHVIDDGIENFSLNMEDLERETENYRRMF 283
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bf5A01    3bf5A02 A:11-37,A:92-107   3bf5A01 A:0-10,A:38-91,A:108-280                      3bf5A02         3bf5A01 A:0-10,A:38-91,A:108-280  [code=3.40.1190.20, no name defined]                                                                                                       --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee.......eeee..eeeeeeehhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh......eeee......eeeeee....eeeeee.hhhhhh.......eeeeee....hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh.......eeeee...eeeeee..eeeeee.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bf5 A   0 GmRFLAYFGHLNIDVLISVDSIPREGSVNVKDLRPRFGGTAGNFAIVAQKFRIPFDLYSAVGmKTHREYLAmIESmGINTGHVEKFEDESGPICYIATDGKKQVSFmHQGAmAAWAPQLADEYEYVHFSTGPNYLDmAKSIRSKIIFDPSQEIHKYSKDELKKFHEISYmSIFNDHEYRVFREmTGLSSPKVTTIVTNGERGSSLFmDGKKYDFPAIPSSGDTVGAGDSFRAGLYLALYNRRSIEKGmIYGTIIAHHVIDDGIENFSLNmEDLERETENYRRmF 283
                             |       9        19        29        39        49        59  |     69 |   |  79        89        99      |109 |     119       129      |139       149       159       169       179   |   189       199      |209       219       229       239       249       259       269       279  | 
                             |                                                           62-MSE   71-MSE                            106-MSE|                      136-MSE                          169-MSE       183-MSE                206-MSE                                  247-MSE               269-MSE      282-MSE
                             1-MSE                                                                    75-MSE                             111-MSE                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with NK_THEAC | Q9HJT3 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:282
                                    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       260       270       280  
             NK_THEAC     1 MRFLAYFGHLNIDVLISVDSIPREGSVNVKDLRPRFGGTAGNFAIVAQKFRIPFDLYSAVGMKTHREYLAMIESMGINTGHVEKFEDESGPICYIATDGKKQVSFMHQGAMEKWKPQLADEYEYVHFSTGPNYLDMAKSIRSKIIFDPSQEIHKYSKDELKKFHEISYMSIFNDHEYRVFREMTGLSSPKVTTIVTNGERGSSLFMDGKKYDFPAIPSSGDTVGAGDSFRAGLYLALYNRRSIEKGMIYGTIIAHHVIDDGIENFSLNMEDLERETENYRRM 282
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -3bf5B01  3bf5B02 B:11-37,B:92-107   3bf5B01 B:2-10,B:38-91,B:108-280                      3bf5B02         3bf5B01 B:2-10,B:38-91,B:108-280  [code=3.40.1190.20, no name defined]                                                                                                       -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...eeeeeee.......eeee..eeeeeeehhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhh......eeee......eeeeee....eeeeeehhhhhh........eeeeee.....hhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh.......eeee.hhh.eeeee..eeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..---.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bf5 B   1 mRFLAYFGHLNIDVLISVDSIPREGSVNVKDLRPRFGGTAGNFAIVAQKFRIPFDLYSAVGmKTHREYLAmIESmGINTGHVEKFEDESGPICYIATDGKKQVSFmHQGAmAAWAPQLADEYEYVHFSTGPNYLDmAKSIRSKIIFDPSQEIHKYSKDELKKFHEISYmSIFNDHEYRVFREmTGLSSPKVTTIVTNGERGSSLFmDGKKYDFPAIPSSGDTVGAGDSFRAGLYLALYNRRSIEKGmIYGTIIAHHVIDDGIE---LNmEDLERETENYRRm 282
                            |       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       260  |   |270       280 |
                            |                                                           62-MSE   71-MSE                            106-MSE|                      136-MSE                          169-MSE       183-MSE                206-MSE                                  247-MSE         263 267 |          282-MSE
                            1-MSE                                                                    75-MSE                             111-MSE                                                                                                                                                       269-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  (0, 0)

(no "SCOP Domain" information available for 3BF5)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BF5)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NK_THEAC | Q9HJT3)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGO  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:90 - Pro A:91   [ RasMol ]  
    Gly B:90 - Pro B:91   [ RasMol ]  
 

(-) 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
  3bf5
    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
  NK_THEAC | Q9HJT3
    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)
  (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
  NK_THEAC | Q9HJT3
    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 3BF5)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BF5)