Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF LOMBRICINE KINASE, COMPLEXED WITH SUBSTRATE ADP
 
Authors :  D. J. Bush, O. Kirillova, S. A. Clark, F. Fabiola, T. Somasundaram, M. S.
Date :  05 Sep 09  (Deposition) - 15 Sep 10  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Mixed Alpha / Beta, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Bush, O. Kirillova, S. A. Clark, O. Davulcu, F. Fabiola, Q. Xie, T. Somasundaram, W. R. Ellington, M. S. Chapman
The Structure Of Lombricine Kinase: Implications For Phosphagen Kinase Conformational Changes.
J. Biol. Chem. V. 286 9338 2011
PubMed-ID: 21212263  |  Reference-DOI: 10.1074/JBC.M110.202796
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LOMBRICINE KINASE
    Chains: A
    EC Number: 2.7.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETBLUE-1
    Expression System Strain: TUNER (DE3)PLACI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: INNKEEPER WORM
    Organism Scientific: URECHIS CAUPO
    Organism Taxid: 6431

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:115 , ARG A:117 , ARG A:119 , HIS A:178 , ARG A:223 , ARG A:279 , SER A:281 , VAL A:282 , HIS A:283 , ARG A:307 , THR A:309 , GLY A:310 , GLY A:311 , GLU A:312 , ASP A:322 , HOH A:465 , HOH A:466BINDING SITE FOR RESIDUE ADP A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JQ3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:198 -Pro A:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JQ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JQ3)

(-) Exons   (0, 0)

(no "Exon" information available for 3JQ3)

(-) 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:364
 aligned with Q8T6T7_URECA | Q8T6T7 from UniProtKB/TrEMBL  Length:366

    Alignment length:364
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362    
         Q8T6T7_URECA     3 FQNDAKANFPDYANHGCVVGRHLNFEMYQRLFGKKTAHGVTVDKVIQPSVDNFGNCIGLIAGDEESYEVFKELFDAVINEKHKGFGPNDSQPAPDLDASKLVGGQFDEKYVKSCRIRTGRGIRGLCYPPSCTRGERREVERVITTALAGLSGDLSGTYYPLSKMTPEQENQLIADHFLFQKPTGHLMVNSASVRDWPDARGIWHNNEKTFLIWINEEDHMRVISMQKGGNVKAVFERFGRGLNAIAEQMKKNGREYMWNQRLGYLCACPSNLGTGLRASVHVQLHQLSKHPKFEDIVVALQLQKRGTGGEHTAAVDDVYDISNAARLKKSEREFVQLLIDGVKKLIDMEQALEAGKSIDDLIPA 366
               SCOP domains d3jq3a1 A:3-89 automated matches                                                       d3jq3a2 A:90-366 automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------ATP-gua_PtransN-3jq3A02 A:12-87                                             -------------------ATP-gua_Ptrans-3jq3A01 A:107-354                                                                                                                                                                                                                        ------------ Pfam domains
         Sec.struct. author ...hhhhhh........hhhhh.hhhhhhhhh........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh..............hhhhh.........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh........hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhh......ee...ee...hhhhh....eeeeeee..hhhhh.hhhhhhhhh.eeee........hhh.eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jq3 A   3 FQNDAKANFPDYANHGCVVGRHLNFEMYQRLFGKKTAHGVTVDKVIQPSVDNFGNCIGLIAGDEESYEVFKELFDAVINEKHKGFGPNDSQPAPDLDASKLVGGQFDEKYVKSCRIRTGRGIRGLCYPPSCTRGERREVERVITTALAGLSGDLSGTYYPLSKMTPEQENQLIADHFLFQKPTGHLMVNSASVRDWPDARGIWHNNEKTFLIWINEEDHMRVISMQKGGNVKAVFERFGRGLNAIAEQMKKNGREYMWNQRLGYLCACPSNLGTGLRASVHVQLHQLSKHPKFEDIVVALQLQKRGTGGEHTAAVDDVYDISNAARLKKSEREFVQLLIDGVKKLIDMEQALEAGKSIDDLIPA 366
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
   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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JQ3)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: GCS (23)
(-)
Clan: no clan defined [family: ATP-gua_PtransN] (14)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8T6T7_URECA | Q8T6T7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    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.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:198 - Pro A:199   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3jq3
    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
  Q8T6T7_URECA | Q8T6T7
    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)
  2.7.3.5
    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
  Q8T6T7_URECA | Q8T6T7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8T6T7_URECA | Q8T6T7: 3jpz

(-) Related Entries Specified in the PDB File

3jpz LOMBRICINE KINASE WITHOUT SUBSTRATES