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

(-) Description

Title :  CRYSTAL STRUCTURE OF AN ARCHAEAL AAA+ ATPASE (SSO1545) FROM SULFOLOBUS SOLFATARICUS P2 AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  10 Jan 06  (Deposition) - 07 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Atp-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, C. L. Rife, D. Carlton, M. D. Miller, S. S. Krishna, M. A. Elsliger P. Abdubek, T. Astakhova, H. J. Chiu, T. Clayton, L. Duan, J. Feuerhelm S. K. Grzechnik, J. Hale, G. W. Han, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, A. Kumar, D. Mcmullan, A. T. Morse, E. Nigoghossian, L. Okach, S. Oommachen, J. Paulsen, R. Reyes, H. Van Den Bedem, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Crystal Structure Of A Novel Archaeal Aaa+ Atpase Sso1545 From Sulfolobus Solfataricus.
Proteins V. 74 1041 2009
PubMed-ID: 19089981  |  Reference-DOI: 10.1002/PROT.22325

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 13814777
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 273057
    Strain: P2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO7Ligand/Ion1,2-ETHANEDIOL
3MG2Ligand/IonMAGNESIUM ION
4MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:43 , ADP A:500 , HOH A:637 , HOH A:668 , HOH A:669 , HOH A:670BINDING SITE FOR RESIDUE MG A 400
02AC2SOFTWARESER B:43 , ADP B:500 , HOH B:666 , HOH B:667 , HOH B:683 , HOH B:684BINDING SITE FOR RESIDUE MG B 400
03AC3SOFTWAREASP A:4 , SER A:6 , PRO A:7 , LYS A:8 , ASP A:13 , PHE A:14 , PHE A:15 , ARG A:39 , THR A:40 , GLY A:41 , LYS A:42 , SER A:43 , SER A:44 , PHE A:216 , PRO A:242 , GLY A:243 , THR A:246 , MG A:400 , EDO A:503 , HOH A:519 , HOH A:616 , HOH A:637 , HOH A:668 , HOH A:670BINDING SITE FOR RESIDUE ADP A 500
04AC4SOFTWAREASP B:4 , THR B:5 , SER B:6 , PRO B:7 , LYS B:8 , PHE B:14 , PHE B:15 , ARG B:39 , THR B:40 , GLY B:41 , LYS B:42 , SER B:43 , SER B:44 , PHE B:216 , PRO B:242 , GLY B:243 , THR B:246 , MG B:400 , HOH B:515 , HOH B:600 , HOH B:628 , HOH B:666 , HOH B:683 , HOH B:684BINDING SITE FOR RESIDUE ADP B 500
05AC5SOFTWAREPRO A:56 , TYR A:57 , LYS A:86 , LEU A:87 , HOH A:579BINDING SITE FOR RESIDUE EDO A 501
06AC6SOFTWARETYR A:183 , ALA A:199 , PHE A:200 , HOH A:627 , PHE B:250 , ILE B:251 , ASP B:254BINDING SITE FOR RESIDUE EDO A 502
07AC7SOFTWAREARG A:39 , GLY A:243 , TYR A:268 , ADP A:500 , HOH A:589BINDING SITE FOR RESIDUE EDO A 503
08AC8SOFTWARELYS A:47 , TYR A:57BINDING SITE FOR RESIDUE EDO A 504
09AC9SOFTWAREASN A:155 , ARG A:187 , ASP A:190 , SER A:193 , PRO A:194BINDING SITE FOR RESIDUE EDO A 505
10BC1SOFTWAREARG A:296 , ALA A:354 , PHE A:355BINDING SITE FOR RESIDUE EDO A 506
11BC2SOFTWARELEU B:121 , SER B:122 , PHE B:123 , ALA B:124 , ALA B:159BINDING SITE FOR RESIDUE EDO B 501

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:301 -B:345

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Mse A:107 -Gly A:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FNA)

(-) 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:352
 aligned with Q97Y08_SULSO | Q97Y08 from UniProtKB/TrEMBL  Length:356

    Alignment length:357
                             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       289       299       309       319       329       339       349       
         Q97Y08_SULSO     - -MLFDTSPKDNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENFLHGREIARKRYLNIMRTLSKCGKWSDVKRALELEEGIEISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLAFS 356
               SCOP domains -d2fnaa2 A:1-283 Archaeal ATPase SSO1545                                                                                                                                                                                                                                                    d2fnaa1 A:284-356 Hypothetical protein SSO1545, C-terminal domain         SCOP domains
               CATH domains 2fnaA01 A:0-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                            2fnaA02 A:208-283  [code=1.10.8.60, no name defined]                        2fnaA03 A:284-356 'winged helix' repressor DNA binding domain             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh..eeeee.hhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhh.....eee....eee.-----..hhhhhhhhhhhh....eeeeee.hhhhhhh....hhhhhhhhhhhh..eeeeeee.hhhhhhhhh..............eeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eee....eee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fna A   0 GmLFDTSPKDNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVImGNEIKFN-----RLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFImSGSEmGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENFLHGREIARKRYLNImRTLSKCGKWSDVKRALELEEGIEISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLAFS 356
                             |       9        19        29        39        49        59        69        79        89        99       109    |    -|      129       139       149       159       169    |  179       189       199       209       219       229       239       249       259       269       279       289     | 299       309       319       329       339       349       
                             |                                                                                                       107-MSE114   120                                                   174-MSE|                                                                                                                 295-MSE                                                         
                             1-MSE                                                                                                                                                                           179-MSE                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with Q97Y08_SULSO | Q97Y08 from UniProtKB/TrEMBL  Length:356

    Alignment length:357
                             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       289       299       309       319       329       339       349       
         Q97Y08_SULSO     - -MLFDTSPKDNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENFLHGREIARKRYLNIMRTLSKCGKWSDVKRALELEEGIEISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLAFS 356
               SCOP domains d2fnab2 B:0-283 Archaeal ATPase SSO1545                                                                                                                                                                                                                                                     d2fnab1 B:284-356 Hypothetical protein SSO1545, C-terminal domain         SCOP domains
               CATH domains 2fnaB01 B:0-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                            2fnaB02 B:208-283  [code=1.10.8.60, no name defined]                        2fnaB03 B:284-356 'winged helix' repressor DNA binding domain             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh..eeeee.hhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhh....eee..eee..-----..hhhhhhhhhhhh....eeeeeehhhhhhhh....hhhhhhhhhhhh..eeeeeee.hhhhhhhhh..............eeee....hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fna B   0 GmLFDTSPKDNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVImGNEIKFN-----RLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFImSGSEmGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENFLHGREIARKRYLNImRTLSKCGKWSDVKRALELEEGIEISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLAFS 356
                             |       9        19        29        39        49        59        69        79        89        99       109    |    -|      129       139       149       159       169    |  179       189       199       209       219       229       239       249       259       269       279       289     | 299       309       319       329       339       349       
                             1-MSE                                                                                                   107-MSE114   120                                                   174-MSE|                                                                                                                 295-MSE                                                         
                                                                                                                                                                                                             179-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: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q97Y08_SULSO | Q97Y08)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Mse A:107 - Gly A:108   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  2fna
    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
  Q97Y08_SULSO | Q97Y08
    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
  Q97Y08_SULSO | Q97Y08
    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 2FNA)

(-) Related Entries Specified in the PDB File

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