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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF NUDIX FAMILY PROTEIN FROM AQUIFEX AEOLICUS
 
Authors :  N. Nakagawa, S. Kishishita, S. Yokoyama, S. Kuramitsu, Riken Structu Genomics/Proteomics Initiative (Rsgi)
Date :  30 Apr 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nudix Family Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nakakaga, S. Kishishita, S. Yokoyama, S. Kuramitsu
Crystal Structure Of Nudix Family Protein From Aquifex Aeolicus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 8-OXO-DGTPASE DOMAIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MUTT
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: MUTT DOMAIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2YYH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro B:35 -Pro B:36
2Pro C:35 -Pro C:36
3Pro D:35 -Pro D:36

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YYH)

(-) 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:138
 aligned with O67435_AQUAE | O67435 from UniProtKB/TrEMBL  Length:139

    Alignment length:138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131        
         O67435_AQUAE     2 GFNVKTPLLATDVIIRLWDGENFKGIVLIERKYPPVGLALPGGFVEVGERVEEAAAREMREETGLEVRLHKLMGVYSDPERDPRAHVVSVVWIGDAQGEPKAGSDAKKVKVYRLEEIPLDKLVFDHKKIILDFLKGNY 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeeeee..eeeeeeeeee......ee..eee.....hhhhhhhhhhhhhhh...eeeeeeeee..........eeeeeeeeeee........eeeeeee.....hhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yyh A   2 GFNVKTPLLATDVIIRLWDGENFKGIVLIERKYPPVGLALPGGFVEVGERVEEAAAREmREETGLEVRLHKLmGVYSDPERDPRAHVVSVVWIGDAQGEPKAGSDAKKVKVYRLEEIPLDKLVFDHKKIILDFLKGNY 139
                                    11        21        31        41        51        61        71  |     81        91       101       111       121       131        
                                                                                     60-MSE        74-MSE                                                             


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with O67435_AQUAE | O67435 from UniProtKB/TrEMBL  Length:139

    Alignment length:138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131        
         O67435_AQUAE     2 GFNVKTPLLATDVIIRLWDGENFKGIVLIERKYPPVGLALPGGFVEVGERVEEAAAREMREETGLEVRLHKLMGVYSDPERDPRAHVVSVVWIGDAQGEPKAGSDAKKVKVYRLEEIPLDKLVFDHKKIILDFLKGNY 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeeeee..eeeeeeeeee.....eee..eee.....hhhhhhhhhhhhhhh...eeeeeeeee..........eeeeeeeeee..........eeeeeehhhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yyh B   2 GFNVKTPLLATDVIIRLWDGENFKGIVLIERKYPPVGLALPGGFVEVGERVEEAAAREmREETGLEVRLHKLmGVYSDPERDPRAHVVSVVWIGDAQGEPKAGSDAKKVKVYRLEEIPLDKLVFDHKKIILDFLKGNY 139
                                    11        21        31        41        51        61        71  |     81        91       101       111       121       131        
                                                                                     60-MSE        74-MSE                                                             


Chain C from PDB  Type:PROTEIN  Length:137
 aligned with O67435_AQUAE | O67435 from UniProtKB/TrEMBL  Length:139

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
         O67435_AQUAE     3 FNVKTPLLATDVIIRLWDGENFKGIVLIERKYPPVGLALPGGFVEVGERVEEAAAREMREETGLEVRLHKLMGVYSDPERDPRAHVVSVVWIGDAQGEPKAGSDAKKVKVYRLEEIPLDKLVFDHKKIILDFLKGNY 139
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeee..eeeeeeeeee......ee..eee.....hhhhhhhhhhhhhhh...eeeeeeeee..........eeeeeeeeee.........eeeeeeehhhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyh C   3 FNVKTPLLATDVIIRLWDGENFKGIVLIERKYPPVGLALPGGFVEVGERVEEAAAREmREETGLEVRLHKLmGVYSDPERDPRAHVVSVVWIGDAQGEPKAGSDAKKVKVYRLEEIPLDKLVFDHKKIILDFLKGNY 139
                                    12        22        32        42        52       |62        72 |      82        92       102       112       122       132       
                                                                                    60-MSE        74-MSE                                                             


Chain D from PDB  Type:PROTEIN  Length:135
 aligned with O67435_AQUAE | O67435 from UniProtKB/TrEMBL  Length:139

    Alignment length:135
                                    14        24        34        44        54        64        74        84        94       104       114       124       134     
         O67435_AQUAE     5 VKTPLLATDVIIRLWDGENFKGIVLIERKYPPVGLALPGGFVEVGERVEEAAAREMREETGLEVRLHKLMGVYSDPERDPRAHVVSVVWIGDAQGEPKAGSDAKKVKVYRLEEIPLDKLVFDHKKIILDFLKGNY 139
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---NUDIX-2yyhD01 D:8-137                                                                                                             -- Pfam domains (1)
           Pfam domains (2) ---NUDIX-2yyhD02 D:8-137                                                                                                             -- Pfam domains (2)
           Pfam domains (3) ---NUDIX-2yyhD03 D:8-137                                                                                                             -- Pfam domains (3)
           Pfam domains (4) ---NUDIX-2yyhD04 D:8-137                                                                                                             -- Pfam domains (4)
         Sec.struct. author ....eeeeeeeeeeee..eeeeeeeeee.....eee..eee.....hhhhhhhhhhhhhhh...eeeeeeeee..........eeeeeeeeeee.........eeeeeehhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yyh D   5 VKTPLLATDVIIRLWDGENFKGIVLIERKYPPVGLALPGGFVEVGERVEEAAAREmREETGLEVRLHKLmGVYSDPERDPRAHVVSVVWIGDAQGEPKAGSDAKKVKVYRLEEIPLDKLVFDHKKIILDFLKGNY 139
                                    14        24        34        44        54     |  64        74        84        94       104       114       124       134     
                                                                                  60-MSE        74-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 2YYH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NUDIX (85)
(-)
Family: NUDIX (78)
(-)
Aquifex aeolicus (1)
1aNUDIX-2yyhD01D:8-137
1bNUDIX-2yyhD02D:8-137
1cNUDIX-2yyhD03D:8-137
1dNUDIX-2yyhD04D:8-137

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O67435_AQUAE | O67435)
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.

 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 2yyh)
 
  Cis Peptide Bonds
    Pro B:35 - Pro B:36   [ RasMol ]  
    Pro C:35 - Pro C:36   [ RasMol ]  
    Pro D:35 - Pro D:36   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  2yyh
    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
  O67435_AQUAE | O67435
    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
  O67435_AQUAE | O67435
    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 2YYH)

(-) Related Entries Specified in the PDB File

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