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 YJEQ FROM AQUIFEX AEOLICUS
 
Authors :  H. Wang, T. Kaminishi, K. Hanawa-Suetsugu, C. Takemoto, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Apr 07  (Deposition) - 15 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Gtpase, Permutation, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, T. Kaminishi, K. Hanawa-Suetsugu, C. Takemoto, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of Yjeq From Aquifex Aeolicus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YJEQ PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET25B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YJEQ
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:257 , HIS A:259 , CYS A:265BINDING SITE FOR RESIDUE ZN A 303
2AC2SOFTWAREHIS A:259 , ALA A:266BINDING SITE FOR RESIDUE CL A 304
3AC3SOFTWAREASN A:118 , LYS A:119 , ASP A:121 , LEU A:122 , SER A:149 , ALA A:150 , LYS A:151 , GLY A:175 , GLY A:177 , LYS A:178 , SER A:179 , SER A:180 , HOH A:1064 , HOH A:1108 , HOH A:1115BINDING SITE FOR RESIDUE GDP A 1001

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:278 -A:299

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:74 -Pro A:75
2Met A:91 -Pro A:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YV5)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_CPPS51721 Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.RSGA_AQUAE69-229  1A:69-229
2ENGC_GTPASEPS50936 EngC GTPase domain profile.RSGA_AQUAE78-227  1A:78-227

(-) Exons   (0, 0)

(no "Exon" information available for 2YV5)

(-) 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:293
 aligned with A4PIH2_AQUAO | A4PIH2 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                    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       290       300  
         A4PIH2_AQUAO     1 MGKKELKRGLVVDREAQMIGVYLFEDGKTYRGIPRGKVLKKTKIYAGDYVWGEVVDPNTFAIEEVEERKNLLIRPKVANVDRVIIVETLKMPEFNNYLLDNMLVVYEYFKVEPVIVFNKIDLLNEEEKKELERWISIYRDAGYDVLKVSAKTGEGIDELVDYLEGFICILAGPSGVGKSSILSRLTGEELRTQEVSEKTERGRHTTTGVRLIPFGKGSFVGDTPGFSKVEATMFVKPREVRNYFREFLRYQCKYPDCTHTNEPGCAVKEAVKNGEISCERYKSYLKIIKVYLEEIKELCRED 302
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------DUF258-2yv5A01 A:131-289                                                                                                                                       ------------- Pfam domains
         Sec.struct. author ......eeeeeeeee..eeeeee.....eeeeee..............eeeeeeee..eeeeeee.....ee....ee...eeeeee.......hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhh...eeeee.....hhhhhhhhhhh........---------....eeeeee...eeee........hhhhh.hhhhhhhhhhhhhhhhhhh..........hhhhhhhhh...hhhhhhhhhhhh.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv5 A   1 MGKKELKRGLVVDREAQMIGVYLFEDGKTYRGIPRGKVLKKTKIYAGDYVWGEVVDPNTFAIEEVEERKNLLIRPKVANVDRVIIVETLKMPEFNNYLLDNMLVVYEYFKVEPVIVFNKIDLLNEEEKKELERWISIYRDAGYDVLKVSAKTGEGIDELVDYLEGFICILAGPSGVGKSSILSRLTGEELRTQEV---------TTTGVRLIPFGKGSFVGDTPGFSKVEATMFVKPREVRNYFREFLRYQCKYPDCTHTNEPGCAVKEAVKNGEISCERYKSYLKIIKVYLEEIKELCRED 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |    -    |  210       220       230       240       250       260       270       280       290       300  
                                                                                                                                                                                                                            195       205                                                                                                 


Chain A from PDB  Type:PROTEIN  Length:293
 aligned with RSGA_AQUAE | O66555 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:302
                                    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       290       300  
           RSGA_AQUAE     1 MGKKELKRGLVVDREAQMIGVYLFEDGKTYRGIPRGKVLKKTKINAGDYVWGEVVDPNTFAIEEVEERKNLLIRPKVANVDRVIIVETLKMPEFNNYLLDNMLVVYEYFKVEPVIVFNKIDLLNEEEKKELERMDSIYRDAGYDVLKVSAKTGEGIDELVDYLEGFICILAGPSGVGKSSILSRLTGEELRTQEVSEKTERGRHTTTGVRLIPFGKGSFVGDTPGFSKVEATMFVKPREVRNYFREFLRYQCKYPDCTHTNEPGCAVKEAVKNGEISCERYKSYLKIIKVYLEEIKELCRED 302
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------DUF258-2yv5A01 A:131-289                                                                                                                                       ------------- Pfam domains
         Sec.struct. author ......eeeeeeeee..eeeeee.....eeeeee..............eeeeeeee..eeeeeee.....ee....ee...eeeeee.......hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhh...eeeee.....hhhhhhhhhhh........---------....eeeeee...eeee........hhhhh.hhhhhhhhhhhhhhhhhhh..........hhhhhhhhh...hhhhhhhhhhhh.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------G_CP  PDB: A:69-229 UniProt: 69-229                                                                                                                              ------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------ENGC_GTPASE  PDB: A:78-227 UniProt: 78-227                                                                                                            --------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv5 A   1 MGKKELKRGLVVDREAQMIGVYLFEDGKTYRGIPRGKVLKKTKIYAGDYVWGEVVDPNTFAIEEVEERKNLLIRPKVANVDRVIIVETLKMPEFNNYLLDNMLVVYEYFKVEPVIVFNKIDLLNEEEKKELERWISIYRDAGYDVLKVSAKTGEGIDELVDYLEGFICILAGPSGVGKSSILSRLTGEELRTQEV---------TTTGVRLIPFGKGSFVGDTPGFSKVEATMFVKPREVRNYFREFLRYQCKYPDCTHTNEPGCAVKEAVKNGEISCERYKSYLKIIKVYLEEIKELCRED 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |    -    |  210       220       230       240       250       260       270       280       290       300  
                                                                                                                                                                                                                            195       205
   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 2YV5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YV5)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (5, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RSGA_AQUAE | O66555)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Chain A   (A4PIH2_AQUAO | A4PIH2)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:74 - Pro A:75   [ RasMol ]  
    Met A:91 - Pro A:92   [ 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
  2yv5
    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
  A4PIH2_AQUAO | A4PIH2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RSGA_AQUAE | O66555
    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
  A4PIH2_AQUAO | A4PIH2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RSGA_AQUAE | O66555
    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 2YV5)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YV5)