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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE THERMOSTABLE JAPANESE FIREFLY LUCIFERASE COMPLEXED WITH MGATP
 
Authors :  T. Nakatsu, S. Ichiyama, J. Hiratake, A. Saldanha, N. Kobashi, K. Sakata, H. Kato, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  31 Aug 05  (Deposition) - 21 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta, Beta Barrel, Alpha+Beta, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nakatsu, S. Ichiyama, J. Hiratake, A. Saldanha, N. Kobashi, K. Sakata, H. Kato
Structural Basis For The Spectral Difference In Luciferase Bioluminescence.
Nature V. 440 372 2006
PubMed-ID: 16541080  |  Reference-DOI: 10.1038/NATURE04542
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LUCIFERIN 4-MONOOXYGENASE
    Chains: A
    EC Number: 1.13.12.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: JAPANESE FIREFLY
    Organism Scientific: LUCIOLA CRUCIATA
    Organism Taxid: 7051
    Synonym: LUCIFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:200 , SER A:201 , HIS A:247 , GLY A:318 , ALA A:319 , PRO A:320 , GLN A:340 , GLY A:341 , TYR A:342 , GLY A:343 , LEU A:344 , THR A:345 , SER A:364 , ASP A:424 , ARG A:439 , LYS A:531 , HOH A:1015 , HOH A:1029 , HOH A:1042 , HOH A:1087BINDING SITE FOR RESIDUE AMP A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D1Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D1Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D1Q)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMP_BINDINGPS00455 Putative AMP-binding domain signature.LUCI_LUCCR197-208  1A:197-208

(-) Exons   (0, 0)

(no "Exon" information available for 2D1Q)

(-) 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:531
 aligned with LUCI_LUCCR | P13129 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:535
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537     
           LUCI_LUCCR     8 ENIVVGPKPFYPIEEGSAGTQLRKYMERYAKLGAIAFTNAVTGVDYSYAEYLEKSCCLGKALQNYGLVVDGRIALCSENCEEFFIPVIAGLFIGVGVAPTNEIYTLRELVHSLGISKPTIVFSSKKGLDKVITVQKTVTTIKTIVILDSKVDYRGYQCLDTFIKRNTPPGFQASSFKTVEVDRKEQVALIMNSSGSTGLPKGVQLTHENTVTRFSHARDPIYGNQVSPGTAVLTVVPFHHGFGMFTTLGYLICGFRVVMLTKFDEETFLKTLQDYKCTSVILVPTLFAILNKSELLNKYDLSNLVEIASGGAPLSKEVGEAVARRFNLPGVRQGYGLTETTSAIIITPEGDDKPGASGKVVPLFKAKVIDLDTKKSLGPNRRGEVCVKGPMLMKGYVNNPEATKELIDEEGWLHTGDIGYYDEEKHFFIVDRLKSLIKYKGYQVPPAELESVLLQHPSIFDAGVAGVPDPVAGELPGAVVVLESGKNMTEKEVMDYVASQVSNAKRLRGGVRFVDEVPKGLTGKIDGRAIREILK 542
               SCOP domains d2d1qa_ A: Luciferase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...........hhhhhhhhhhhhhhhhh.eeeee.....eeehhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eeee...........hhhhhhhhh.....hhhhh..........eeeee...----....eeeehhhhhhhhhhhh............eeee.....hhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh...eeee.hhhhhhhhhh.hhhhh......eeee.....hhhhhhhhhhhh.....eeeee.hhhh.eeee............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee.hhheee..eeehhhhhhhhhhh...eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhh..hhhhh....eee............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1q A   8 ENIVVGPKPFYPIEEGSAGTQLRKYMERYAKLGAIAFTNAVTGVDYSYAEYLEKSccLGKALQNYGLVVDGRIALCSENCEEFFIPVIAGLFIGVGVAPTNEIYTLRELVHSLGISKPTIVFSSKKGLDKVITVQKTVTTIKTIVILDSKVDYRGYQCLDTFIKRNTPPGFQASSFKTVEVDRKEQVALIMNSS----LPKGVQLTHENIVTRFSHARDPIYGNQVSPGTAVLTVVPFHHGFGMFTTLGYLICGFRVVMLTKFDEETFLKTLQDYKCTSVILVPTLFAILNKSELLNKYDLSNLVEIASGGAPLSKEVGEAVARRFNLPGVRQGYGLTETTSAIIITPEGDDKPGASGKVVPLFKAKVIDLDTKKSLGPNRRGEVCVKGPMLMKGYVNNPEATKELIDEEGWLHTGDIGYYDEEKHFFIVDRLKSLIKYKGYQVPPAELESVLLQHPSIFDAGVAGVPDPVAGELPGAVVVLESGKNMTEKEVMDYVASQVSNAKRLRGGVRFVDEVPKGLTGKIDGRAIREILK 542
                                    17        27        37        47        57     || 67        77        87        97       107       117       127       137       147       157       167       177       187       197   |   207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537     
                                                                                  63-CSO                                                                                                                                   201  206                                                                                                                                                                                                                                                                                                                                                
                                                                                   64-CSO
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D1Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D1Q)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LUCI_LUCCR | P13129)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0047077    Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity    Catalysis of the reaction: O2 + ATP + Photinus luciferin = light + diphosphate + AMP + CO2 + oxidized Photinus luciferin.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

 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
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CSO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2d1q)
 

(-) 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
  2d1q
    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
  LUCI_LUCCR | P13129
    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)
  1.13.12.7
    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
  LUCI_LUCCR | P13129
    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
        LUCI_LUCCR | P13129: 2d1r 2d1s 2d1t

(-) Related Entries Specified in the PDB File

2d1r
2d1s
2d1t RELATED ID: MY_001000084.1 RELATED DB: TARGETDB