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 :  ABC PROTEIN ARTP IN COMPLEX WITH ADP-BETA-S
 
Authors :  P. F. Thaben, V. Eckey, F. Scheffel, W. Saenger, E. Schneider, A. Vahedi-Faridi
Date :  19 Jan 07  (Deposition) - 15 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Abc Domain, Atpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. F. Thaben, V. Eckey, F. Scheffel, W. Saenger, E. Schneider, A. Vahedi-Faridi
Crystal Structures Of The Atp-Binding Cassette (Abc) Protein Artp From Geobacillus Stearothermophilus Reveal A Stable Dimer In The Post Hydrolysis State And An Asymmetry In The Dimerization Region
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINO ACID ABC TRANSPORTER
    Chains: A, B, C, D
    EC Number: 3.6.3.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARTP
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: DSMZ 13240
    Synonym: ATP-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1AT44Ligand/Ion5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:11 , VAL A:16 , GLY A:37 , SER A:38 , GLY A:39 , LYS A:40 , SER A:41 , THR A:42 , HOH A:622 , HOH A:711 , HOH A:716 , HOH A:733 , HOH A:738BINDING SITE FOR RESIDUE AT4 A 601
2AC2SOFTWAREPHE B:11 , VAL B:16 , SER B:36 , GLY B:37 , SER B:38 , GLY B:39 , LYS B:40 , SER B:41 , THR B:42 , HOH B:616 , HOH B:662BINDING SITE FOR RESIDUE AT4 B 602
3AC3SOFTWAREGLY B:173 , LEU B:176 , GLU B:195 , PHE C:11 , VAL C:16 , SER C:36 , GLY C:37 , SER C:38 , GLY C:39 , LYS C:40 , SER C:41 , THR C:42 , HOH C:640 , HOH C:694 , HOH C:706 , HOH C:709BINDING SITE FOR RESIDUE AT4 C 603
4AC4SOFTWAREASP A:122 , PHE D:11 , LEU D:14 , VAL D:16 , GLY D:37 , SER D:38 , GLY D:39 , LYS D:40 , SER D:41 , THR D:42 , HOH D:624BINDING SITE FOR RESIDUE AT4 D 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OLK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OLK)

(-) 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:242
 aligned with D0VWX4_GEOSE | D0VWX4 from UniProtKB/TrEMBL  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
         D0VWX4_GEOSE     2 LQMIDVHQLKKSFGSLEVLKGINVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTNLNKVREEVGMVFQRFNLFPHMTVLNNITLAPMKVRKWPREKAEAKAMELLDKVGLKDKAHAYPDSLSGGQAQRVAIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEMGFAREVGDRVLFMDGGYIIEEGKPEDLFDRPQHERTKAFLSKVF 243
               SCOP domains d2olka_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2olkA00 A:-1-240 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeeeeeeee....eeeee.....hhhhhhhhhh......eeeeee..ee...hhhhhhhhhhheeee..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.eeeeee..eeeeeehhhhhhhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olk A  -1 LQMIDVHQLKKSFGSLEVLKGINVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTNLNKVREEVGMVFQRFNLFPHMTVLNNITLAPMKVRKWPREKAEAKAMELLDKVGLKDKAHAYPDSLSGGQAQRVAIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEMGFAREVGDRVLFMDGGYIIEEGKPEDLFDRPQHERTKAFLSKVF 240
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238  


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with D0VWX4_GEOSE | D0VWX4 from UniProtKB/TrEMBL  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
         D0VWX4_GEOSE     2 LQMIDVHQLKKSFGSLEVLKGINVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTNLNKVREEVGMVFQRFNLFPHMTVLNNITLAPMKVRKWPREKAEAKAMELLDKVGLKDKAHAYPDSLSGGQAQRVAIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEMGFAREVGDRVLFMDGGYIIEEGKPEDLFDRPQHERTKAFLSKVF 243
               SCOP domains d2olkb_ B: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2olkB00 B:-1-240 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeeeeeeee....eeeee.....hhhhhhhhhh......eeeeee..ee......hhhhhhhheeee..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.eeeeee..eeeeeehhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olk B  -1 LQMIDVHQLKKSFGSLEVLKGINVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTNLNKVREEVGMVFQRFNLFPHMTVLNNITLAPMKVRKWPREKAEAKAMELLDKVGLKDKAHAYPDSLSGGQAQRVAIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEMGFAREVGDRVLFMDGGYIIEEGKPEDLFDRPQHERTKAFLSKVF 240
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238  


Chain C from PDB  Type:PROTEIN  Length:242
 aligned with D0VWX4_GEOSE | D0VWX4 from UniProtKB/TrEMBL  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
         D0VWX4_GEOSE     2 LQMIDVHQLKKSFGSLEVLKGINVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTNLNKVREEVGMVFQRFNLFPHMTVLNNITLAPMKVRKWPREKAEAKAMELLDKVGLKDKAHAYPDSLSGGQAQRVAIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEMGFAREVGDRVLFMDGGYIIEEGKPEDLFDRPQHERTKAFLSKVF 243
               SCOP domains d2olkc_ C: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2olkC00 C:-1-240 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeeeeeeee....eeeee.....hhhhhhhhhh......eeeeee..ee...hhhhhhhhhhheeee..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.eeeeee..eeeeeehhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olk C  -1 LQMIDVHQLKKSFGSLEVLKGINVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTNLNKVREEVGMVFQRFNLFPHMTVLNNITLAPMKVRKWPREKAEAKAMELLDKVGLKDKAHAYPDSLSGGQAQRVAIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEMGFAREVGDRVLFMDGGYIIEEGKPEDLFDRPQHERTKAFLSKVF 240
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238  


Chain D from PDB  Type:PROTEIN  Length:242
 aligned with D0VWX4_GEOSE | D0VWX4 from UniProtKB/TrEMBL  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
         D0VWX4_GEOSE     2 LQMIDVHQLKKSFGSLEVLKGINVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTNLNKVREEVGMVFQRFNLFPHMTVLNNITLAPMKVRKWPREKAEAKAMELLDKVGLKDKAHAYPDSLSGGQAQRVAIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEMGFAREVGDRVLFMDGGYIIEEGKPEDLFDRPQHERTKAFLSKVF 243
               SCOP domains d2olkd_ D: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2olkD00 D:-1-240 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee....eeeee.....hhhhhhhhhh......eeeeee..ee......hhhhhhhheeee..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.eeeeee..eeeeeehhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olk D  -1 LQMIDVHQLKKSFGSLEVLKGINVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTNLNKVREEVGMVFQRFNLFPHMTVLNNITLAPMKVRKWPREKAEAKAMELLDKVGLKDKAHAYPDSLSGGQAQRVAIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEMGFAREVGDRVLFMDGGYIIEEGKPEDLFDRPQHERTKAFLSKVF 240
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (D0VWX4_GEOSE | D0VWX4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0015424    amino acid-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + amino acid(out/in) = ADP + phosphate + amino acid(in/out).
    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.
    GO:0015426    polar-amino acid-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + polar amino acid(out) = ADP + phosphate + polar amino acid(in).
biological process
    GO:0003333    amino acid transmembrane transport    The directed movement of amino acids, organic acids containing one or more amino substituents across a membrane by means of some agent such as a transporter or pore.

 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
    AT4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2olk)
 

(-) 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
  2olk
    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
  D0VWX4_GEOSE | D0VWX4
    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)
  3.6.3.21
    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
  D0VWX4_GEOSE | D0VWX4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D0VWX4_GEOSE | D0VWX4: 2olj 2ouk 2q0h 3c41 3c4j

(-) Related Entries Specified in the PDB File

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