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 :  D202K MUTANT OF P. DENITRIFICANS ATP12P
 
Authors :  D. L. Gatti, A. Ludlam, J. Brunzelle, S. H. Ackerman
Date :  19 Nov 07  (Deposition) - 25 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Atpase Chaperone F1 Assembly, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ludlam, J. Brunzelle, T. Pribyl, X. Xu, D. L. Gatti, S. H. Ackerman
Chaperones Of F1-Atpase
J. Biol. Chem. V. 284 17138 2009
PubMed-ID: 19383603  |  Reference-DOI: 10.1074/JBC.M109.002568

(-) Compounds

Molecule 1 - ATP12 ATPASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-ATP12D202K
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Gene: PDEN_0792
    Mutation: YES
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 318586
    Strain: PD1222

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2ZD2)

(-) Sites  (0, 0)

(no "Site" information available for 2ZD2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZD2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:1108 -Pro A:1109
2Ala B:2108 -Pro B:2109

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZD2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZD2)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZD2)

(-) 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:234
 aligned with A1B060_PARDP | A1B060 from UniProtKB/TrEMBL  Length:236

    Alignment length:234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
        A1B060_PARDP      2 SEWKARRFWASVGIHKEEGGWAVLLDERPLRTPGKQPLRLPTEALALAIAEEWQAVQEVIDPNAMPLTRSANSAIEKVAPQFDAVAAMLGDYGGTDLLSYRADAPEALVRAQAEGWDPLIDWAATELRAPLRITHGVIPVPQDPVVLLKLRAEVASLDPFGLTALHDLVTLPGSLILGLAVIRGRIDAPTAHALSRIDEEFQAERWGRDEEAEAQAASRLAAMRDSERFWHLTR  235
               SCOP domains d2zd2a1 A:1005-1238 ATP12 ATPase                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.....eeee......eeee..ee............hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhhhh......ee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2zd2 A 1005 SEWKARRFWASVGIHKEEGGWAVLLDERPLRTPGKQPLRLPTEALALAIAEEWQAVQEVIDPNAMPLTRSANSAIEKVAPQFDAVAAMLGDYGGTDLLSYRADAPEALVRAQAEGWDPLIDWAATELRAPLRITHGVIPVPQDPVVLLKLRAEVASLDPFGLTALHDLVTLPGSLILGLAVIRGRIDAPTAHALSRIKEEFQAERWGRDEEAEAQAASRLAAMRDSERFWHLTR 1238
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234    


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with A1B060_PARDP | A1B060 from UniProtKB/TrEMBL  Length:236

    Alignment length:234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
        A1B060_PARDP      2 SEWKARRFWASVGIHKEEGGWAVLLDERPLRTPGKQPLRLPTEALALAIAEEWQAVQEVIDPNAMPLTRSANSAIEKVAPQFDAVAAMLGDYGGTDLLSYRADAPEALVRAQAEGWDPLIDWAATELRAPLRITHGVIPVPQDPVVLLKLRAEVASLDPFGLTALHDLVTLPGSLILGLAVIRGRIDAPTAHALSRIDEEFQAERWGRDEEAEAQAASRLAAMRDSERFWHLTR  235
               SCOP domains d2zd2b_ B: ATP12 ATPase                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----ATP12-2zd2B01 B:2010-2131                                                                                                 ----------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----ATP12-2zd2B02 B:2010-2131                                                                                                 ----------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhh.....eeeee....eeeee..ee.ee...ee....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhhhh......ee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2zd2 B 2005 SEWKARRFWASVGIHKEEGGWAVLLDERPLRTPGKQPLRLPTEALALAIAEEWQAVQEVIDPNAMPLTRSANSAIEKVAPQFDAVAAMLGDYGGTDLLSYRADAPEALVRAQAEGWDPLIDWAATELRAPLRITHGVIPVPQDPVVLLKLRAEVASLDPFGLTALHDLVTLPGSLILGLAVIRGRIDAPTAHALSRIKEEFQAERWGRDEEAEAQAASRLAAMRDSERFWHLTR 2238
                                  2014      2024      2034      2044      2054      2064      2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174      2184      2194      2204      2214      2224      2234
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZD2)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: ATP12] (2)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A1B060_PARDP | A1B060)
biological process
    GO:0043461    proton-transporting ATP synthase complex assembly    The aggregation, arrangement and bonding together of a proton-transporting ATP synthase (also known as F-type ATPase), a two-sector ATPase found in the inner membrane of mitochondria and chloroplasts, and in bacterial plasma membranes.

 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
(no "Ligands, Modified Residues, Ions" information available for 2zd2)
 
  Sites
(no "Sites" information available for 2zd2)
 
  Cis Peptide Bonds
    Ala A:1108 - Pro A:1109   [ RasMol ]  
    Ala B:2108 - Pro B:2109   [ 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
  2zd2
    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
  A1B060_PARDP | A1B060
    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
  A1B060_PARDP | A1B060
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A1B060_PARDP | A1B060: 2p4x 2r31

(-) Related Entries Specified in the PDB File

2p4x 2r31