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 :  ADP IN TRANSITION BINDING SITE IN THE SUBUNIT B OF THE ENERGY CONVERTER A1AO ATP SYNTHASE
 
Authors :  A. Kumar, S. M. S. Manimekalai, A. M. Balakrishna, G. Gruber
Date :  14 Jul 08  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Atp Synthesis, Hydrogen Ion Transport, Ion Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumar, M. S. Manimekalai, G. Gruber
Structure Of The Nucleotide-Binding Subunit B Of The Energy Producer A1A0 Atp Synthase In Complex With Adenosine Diphosphate
Acta Crystallogr. , Sect. D V. 64 1110 2008
PubMed-ID: 19020348  |  Reference-DOI: 10.1107/S090744490802790X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - V-TYPE ATP SYNTHASE BETA CHAIN
    Chains: A, B
    EC Number: 3.6.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9D-HIS6
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ATP SYNTHASE
    Organism Common: METHANOSARCINA FRISIA
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 2209
    Strain: GO1
    Synonym: V-TYPE ATPASE SUBUNIT B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:149 , LEU A:303 , SER A:304 , MET A:305 , PRO A:315 , LEU A:317 , SER A:318 , ILE A:321 , GLN A:325 , PRO A:345 , HOH A:660 , PHE B:149 , ILE B:321 , GLN B:325 , PRO B:345BINDING SITE FOR RESIDUE ADP A 461

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DSR)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asp A:215 -Pro A:216
2Met A:305 -Pro A:306
3Ile A:314 -Pro A:315
4Tyr A:338 -Pro A:339
5Gly B:13 -Pro B:14
6Tyr B:338 -Pro B:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DSR)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATPASE_ALPHA_BETAPS00152 ATP synthase alpha and beta subunits signature.VATB_METMA339-348
 		  2A:339-348
B:339-348

(-) Exons   (0, 0)

(no "Exon" information available for 3DSR)

(-) 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:419
 aligned with VATB_METMA | Q60187 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:446
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      
           VATB_METMA    12 AGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEGTGGLDKDCGVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 457
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeee.....eeeeeeeee...eeeeee...----------..eee..ee..hhhhh..ee..................ee................ee...hhhhhh...ee......ee.....hhhhhhhhhhhhh.......eeeeeeeeeeehhhhhhhhhhhhhhh.hhh.eeeeeee....hhhhhhhhhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhh...-----------...hhhhhhhhhh..ee......eeeeeeee...------....hhhhh..eeeeehhhhhh......eeeeeeee.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsr A  12 AGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEG----------IFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGA-----------PGYMYTDLATLYERAGIVKGAKGSVTQIPILSMP------PIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 457
                                    21        31        41        51       | -        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         - |     281       291       301    |    - |     321       331       341       351       361       371       381       391       401       411       421       431       441       451      
                                                                          59         70                                                                                                                                                                                            261         273                              306    313                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:425
 aligned with VATB_METMA | Q60187 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:446
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450      
           VATB_METMA    11 IAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEGTGGLDKDCGVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAH 456
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.........eeeee.....eeeeeeeee...eeeeee..---------....eee..eeeehhhhh.eeee...............eeee................ee...hhhhhh...ee......ee.....hhhhhhhhhhhhh........eeeeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.....------......hhhhhhhhhhh..ee......eeeeeeee..------.....hhhhh..eeee.hhhhhhh...........ee.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsr B  11 IAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFE---------GVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAA------RRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSM------HPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAH 456
                                    20        30        40        50       | -       |70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 |     270       280       290       300    |    - |     320       330       340       350       360       370       380       390       400       410       420       430       440       450      
                                                                          58        68                                                                                                                                                                                               262    269                                 305    312
   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 3DSR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DSR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DSR)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VATB_METMA | Q60187)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016820    hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances    Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane.
    GO:0046933    proton-transporting ATP synthase activity, rotational mechanism    Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ADP + H2O + phosphate + H+(in) = ATP + H+(out), by a rotational mechanism.
biological process
    GO:0006754    ATP biosynthetic process    The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0015991    ATP hydrolysis coupled proton transport    The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis.
    GO:0046034    ATP metabolic process    The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0015986    ATP synthesis coupled proton transport    The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0042777    plasma membrane ATP synthesis coupled proton transport    The transport of protons across the plasma membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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.
cellular component
    GO:0033178    proton-transporting two-sector ATPase complex, catalytic domain    A protein complex that forms part of a proton-transporting two-sector ATPase complex and catalyzes ATP hydrolysis or synthesis. The catalytic domain (F1, V1, or A1) comprises a hexameric catalytic core and a central stalk, and is peripherally associated with the membrane when the two-sector ATPase is assembled.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:215 - Pro A:216   [ RasMol ]  
    Gly B:13 - Pro B:14   [ RasMol ]  
    Ile A:314 - Pro A:315   [ RasMol ]  
    Met A:305 - Pro A:306   [ RasMol ]  
    Tyr A:338 - Pro A:339   [ RasMol ]  
    Tyr B:338 - Pro B:339   [ 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
  3dsr
    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
  VATB_METMA | Q60187
    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)
  3.6.3.14
    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
  VATB_METMA | Q60187
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VATB_METMA | Q60187: 2c61 2rkw 3b2q 3eiu 3ssa 3tgw 3tiv

(-) Related Entries Specified in the PDB File

2c61 2rkw 3b2q