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 :  PHOSPHOTRANSFERASE
 
Authors :  M. B. Berry, G. N. Phillips Jr.
Date :  07 Jun 96  (Deposition) - 07 Jul 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphotransferase, Zinc Finger, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Berry, G. N. Phillips Jr.
Crystal Structures Of Bacillus Stearothermophilus Adenylate Kinase With Bound Ap5A, Mg2+ Ap5A, And Mn2+ Ap5A Reveal An Intermediate Lid Position And Six Coordinate Octahedral Geometry For Bound Mg2+ And Mn2+.
Proteins V. 32 276 1998 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENYLATE KINASE
    Chains: A
    EC Number: 2.7.4.3
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Other Details: ZINC FINGER
    Synonym: ADK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AP51Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:130 , CYS A:133 , CYS A:150 , CYS A:153BINDING SITE FOR RESIDUE ZN A 219
2AC2SOFTWAREAP5 A:218 , HOH A:300 , HOH A:301 , HOH A:302 , HOH A:303BINDING SITE FOR RESIDUE MG A 220
3AC3SOFTWAREPRO A:9 , GLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , GLY A:14 , THR A:15 , THR A:31 , GLY A:32 , ARG A:36 , MET A:53 , ASP A:57 , VAL A:59 , GLY A:85 , ARG A:88 , GLN A:92 , ARG A:123 , LEU A:124 , ARG A:127 , THR A:136 , TYR A:137 , HIS A:138 , ARG A:160 , ARG A:171 , GLN A:199 , MG A:220 , HOH A:300 , HOH A:302 , HOH A:303 , HOH A:305 , HOH A:326 , HOH A:364 , HOH A:376 , HOH A:444 , HOH A:468 , HOH A:481BINDING SITE FOR RESIDUE AP5 A 218

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZIO)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:86 -Pro A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZIO)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD_GEOSE81-92  1A:81-92

(-) Exons   (0, 0)

(no "Exon" information available for 1ZIO)

(-) 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:217
 aligned with KAD_GEOSE | P27142 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
            KAD_GEOSE     1 MNLVLMGLPGAGKGTQAEKIVAAYGIPHISTGDMFRAAMKEGTPLGLQAKQYMDRGDLVPDEVTIGIVRERLSKDDCQNGFLLDGFPRTVAQAEALETMLADIGRKLDYVIHIDVRQDVLMERLTGRRICRNCGATYHLIFHPPAKPGVCDKCGGELYQRADDNEATVANRLEVNMKQMKPLVDFYEQKGYLRNINGEQDMEKVFADIRELLGGLAR 217
               SCOP domains d1zioa1 A:1-125,A:161-217 Adenylate kinase                                                                                   d1zioa2 A:126-160                  d1zioa1 A:1-125,A:161-217 Adenylate kinase                SCOP domains
               CATH domains 1zioA00 A:1-217 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh..eeeehhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhh..hhh...eeee.....hhhhhhhhhhhhhh.....eeeeee..hhhhhhhhh.eee......eee......................hhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zio A   1 MNLVLMGLPGAGKGTQAEKIVAAYGIPHISTGDMFRAAMKEGTPLGLQAKQYMDRGDLVPDEVTIGIVRERLSKDDCQNGFLLDGFPRTVAQAEALETMLADIGRKLDYVIHIDVRQDVLMERLTGRRICRNCGATYHLIFHPPAKPGVCDKCGGELYQRADDNEATVANRLEVNMKQMKPLVDFYEQKGYLRNINGEQDMEKVFADIRELLGGLAR 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZIO)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KAD_GEOSE | P27142)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004017    adenylate kinase activity    Catalysis of the reaction: ATP + AMP = 2 ADP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019205    nucleobase-containing compound kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate.
    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:0016776    phosphotransferase activity, phosphate group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a phosphate group (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    AP5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:86 - Pro A:87   [ 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
  1zio
    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
  KAD_GEOSE | P27142
    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)
  2.7.4.3
    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
  KAD_GEOSE | P27142
    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
        KAD_GEOSE | P27142: 1zin 1zip 4qbh 4qbi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ZIO)