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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARCHAEAL SECRETION ATPASE GSPE IN COMPLEX WITH AMP-PNP
 
Authors :  A. Yamagata, J. A. Tainer
Date :  17 Dec 06  (Deposition) - 13 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  1,2
Biol. Unit 1:  1,2  (3x)
Keywords :  Hexameric Atpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yamagata, J. A. Tainer
Hexameric Structures Of The Archaeal Secretion Atpase Gspe And Implications For A Universal Secretion Mechanism.
Embo J. V. 26 878 2007
PubMed-ID: 17255937  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601544

(-) Compounds

Molecule 1 - TYPE II SECRETION SYSTEM PROTEIN
    Chains: 1, 2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304
    Synonym: GSPE-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : 12
Biological Unit 1 (3x): 12

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 36)

Asymmetric Unit (3, 36)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3MSE33Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 105)
No.NameCountTypeFull Name
1ANP6Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3MSE99Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR 2:274 , ANP 2:513BINDING SITE FOR RESIDUE MG 2 512
2AC2SOFTWARELEU 1:239 , THR 1:244 , ALA 1:270 , SER 1:271 , GLY 1:272 , LYS 1:273 , THR 1:274 , THR 1:275 , GLU 1:298 , GLU 1:341 , THR 1:363 , ARG 1:408BINDING SITE FOR RESIDUE ANP 1 512
3AC3SOFTWAREARG 2:208 , ARG 2:227 , LYS 2:228 , THR 2:230 , LEU 2:234 , LYS 2:242 , THR 2:269 , ALA 2:270 , SER 2:271 , GLY 2:272 , LYS 2:273 , THR 2:274 , THR 2:275 , GLU 2:341 , ARG 2:408 , MG 2:512BINDING SITE FOR RESIDUE ANP 2 513

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu 1:38 -Pro 1:39
2Glu 1:379 -Pro 1:380
3Glu 2:38 -Pro 2:39
4Glu 2:379 -Pro 2:380

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OAP)

(-) 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 1 from PDB  Type:PROTEIN  Length:498
 aligned with O29598_ARCFU | O29598 from UniProtKB/TrEMBL  Length:511

    Alignment length:507
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       
         O29598_ARCFU     5 HYDILRRHIRSEDLLETPEFGSGSRIVEEYWIQEPFTKAIIVENEDEFRNVYYALEPTVSSEEAEVISALYDDLKKILVLQDVSVDLEERAEVLVRAIEKLSKEYAVSFTDNFYSRMLYYLFRDFFGYGLIDPLMEDTNVEDISCDGYNIPIFIYHQKYGNVETNIVLDQEKLDRMVLRLTQRSGKHISIANPIVDATLPDGSRLQATFGTEVTPRGSSFTIRKFTIEPLTPIDLIEKGTVPSGVLAYLWLAIEHKFSAIVVGETASGKTTTLNAIMMFIPPDAKVVSIEDTREIKLYHENWIAEVTRTGMGEGEIDMYDLLRAALRQRPDYIIVGEVRGREAQTLFQAMSTGHASYSTLHAGDINQMVYRLESEPLKVPRSMLQFLDIALVQTMWVRGNTRLRRTKEVNEILGIDPVDKNLLVNQFVKWDPKEDKHIEVSMPKKLEKMADFLGVSVQEVYDEMLSRKRYLELMLKRGIRNYKEVTRYIHAYYRNPELAMTKMEEGL 511
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................eeeeeeee...eeeeee........eeeee....hhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh---------....hhhhhhhhhhh...hhhhhhhhhh..eeeeee.......eeee...eeee.....hhhhhhhhhhhhhhhh.........eeeeee...eeeeee..........eeeeee......hhhhhhhh...hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh.....eeeee...........eeeee..........hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh.....hhhhhhhh.eeeeeeeee....eeeeeeeeeeeee........eeeeeeeee....eeee....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oap 1   5 HYDILRRHIRSEDLLETPEFGSGSRIVEEYWIQEPFTKAIIVENEDEFRNVYYALEPTVSSEEAEVISALYDDLKKILVLQDVSVDLEERAEVLVRAIEK---------TDNFYSRmLYYLFRDFFGYGLIDPLmEDTNVEDISCDGYNIPIFIYHQKYGNVETNIVLDQEKLDRmVLRLTQRSGKHISIANPIVDATLPDGSRLQATFGTEVTPRGSSFTIRKFTIEPLTPIDLIEKGTVPSGVLAYLWLAIEHKFSAIVVGETASGKTTTLNAImmFIPPDAKVVSIEDTREIKLYHENWIAEVTRTGmGEGEIDmYDLLRAALRQRPDYIIVGEVRGREAQTLFQAmSTGHASYSTLHAGDINQmVYRLESEPLKVPRSmLQFLDIALVQTmWVRGNTRLRRTKEVNEILGIDPVDKNLLVNQFVKWDPKEDKHIEVSmPKKLEKmADFLGVSVQEVYDEmLSRKRYLELmLKRGIRNYKEVTRYIHAYYRNPELAmTKmEEGL 511
                                    14        24        34        44        54        64        74        84        94       104       114      |124       134    |  144       154       164       174     | 184       194       204       214       224       234       244       254       264       274      |284       294       304       314|      324       334       344       354       364       374       384  |    394    |  404       414       424       434       444 |     454       464   |   474   |   484       494       504  |    
                                                                                                                             104       114      |               139-MSE                                  180-MSE                                                                                              281-MSE                           315-MSE  |                             354-MSE           372-MSE        387-MSE     399-MSE                                        446-MSE  |            468-MSE   478-MSE                   504-MSE   
                                                                                                                                              121-MSE                                                                                                                                                          282-MSE                                 322-MSE                                                                                                                            453-MSE                                               507-MSE


Chain 2 from PDB  Type:PROTEIN  Length:503
 aligned with O29598_ARCFU | O29598 from UniProtKB/TrEMBL  Length:511

    Alignment length:507
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       
         O29598_ARCFU     5 HYDILRRHIRSEDLLETPEFGSGSRIVEEYWIQEPFTKAIIVENEDEFRNVYYALEPTVSSEEAEVISALYDDLKKILVLQDVSVDLEERAEVLVRAIEKLSKEYAVSFTDNFYSRMLYYLFRDFFGYGLIDPLMEDTNVEDISCDGYNIPIFIYHQKYGNVETNIVLDQEKLDRMVLRLTQRSGKHISIANPIVDATLPDGSRLQATFGTEVTPRGSSFTIRKFTIEPLTPIDLIEKGTVPSGVLAYLWLAIEHKFSAIVVGETASGKTTTLNAIMMFIPPDAKVVSIEDTREIKLYHENWIAEVTRTGMGEGEIDMYDLLRAALRQRPDYIIVGEVRGREAQTLFQAMSTGHASYSTLHAGDINQMVYRLESEPLKVPRSMLQFLDIALVQTMWVRGNTRLRRTKEVNEILGIDPVDKNLLVNQFVKWDPKEDKHIEVSMPKKLEKMADFLGVSVQEVYDEMLSRKRYLELMLKRGIRNYKEVTRYIHAYYRNPELAMTKMEEGL 511
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------T2SE-2oap201 2:132-400                                                                                                                                                                                                                                                       --------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------T2SE-2oap202 2:132-400                                                                                                                                                                                                                                                       --------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhh...............eeeeeeeee...eeeeeeeehhhhee..eee....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeeeee.......eeee...eeee.....hhhhhhhhhhhhhhh..........eeeee.....eeeee..........eeeee.......hhhhhhhh...hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh.....eeeee...........eeeee....----..hhhhhhhhhh.....eee......hhhhhhhhhhhh..eeeeeee...hhhhhhhhhh.....hhhhhhhh.eeeeeeeee....eeeeeeeeeeeeee......eeeeeeeeee....eeee....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oap 2   5 HYDILRRHIRSEDLLETPEFGSGSRIVEEYWIQEPFTKAIIVENEDEFRNVYYALEPTVSSEEAEVISALYDDLKKILVLQDVSVDLEERAEVLVRAIEKLSKEYAVSFTDNFYSRmLYYLFRDFFGYGLIDPLmEDTNVEDISCDGYNIPIFIYHQKYGNVETNIVLDQEKLDRmVLRLTQRSGKHISIANPIVDATLPDGSRLQATFGTEVTPRGSSFTIRKFTIEPLTPIDLIEKGTVPSGVLAYLWLAIEHKFSAIVVGETASGKTTTLNAImmFIPPDAKVVSIEDTREIKLYHENWIAEVTRTG----EIDmYDLLRAALRQRPDYIIVGEVRGREAQTLFQAmSTGHASYSTLHAGDINQmVYRLESEPLKVPRSmLQFLDIALVQTmWVRGNTRLRRTKEVNEILGIDPVDKNLLVNQFVKWDPKEDKHIEVSmPKKLEKmADFLGVSVQEVYDEmLSRKRYLELmLKRGIRNYKEVTRYIHAYYRNPELAmTKmEEGL 511
                                    14        24        34        44        54        64        74        84        94       104       114      |124       134    |  144       154       164       174     | 184       194       204       214       224       234       244       254       264       274      |284       294       304       314    |  324       334       344       354       364       374       384  |    394    |  404       414       424       434       444 |     454       464   |   474   |   484       494       504  |    
                                                                                                                                              121-MSE           139-MSE                                  180-MSE                                                                                              281-MSE                          314  319  |                             354-MSE           372-MSE        387-MSE     399-MSE                                        446-MSE  |            468-MSE   478-MSE                   504-MSE   
                                                                                                                                                                                                                                                                                                               282-MSE                                 322-MSE                                                                                                                            453-MSE                                               507-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 2OAP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain 1,2   (O29598_ARCFU | O29598)
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.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

 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
    ANP  [ 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 ]
 
  Cis Peptide Bonds
    Glu 1:379 - Pro 1:380   [ RasMol ]  
    Glu 1:38 - Pro 1:39   [ RasMol ]  
    Glu 2:379 - Pro 2:380   [ RasMol ]  
    Glu 2:38 - Pro 2:39   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  2oap
    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
  O29598_ARCFU | O29598
    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
  O29598_ARCFU | O29598
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O29598_ARCFU | O29598: 2oaq

(-) Related Entries Specified in the PDB File

2oaq