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 :  CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH 3-DEAZAURIDINE 5'-MONOPHOSPHATE
 
Authors :  A. A. Fedorov, E. V. Fedorov, V. Iiams, J. A. Gerlt, S. C. Almo
Date :  29 Nov 13  (Deposition) - 18 Dec 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim-Barrel, Orotidine 5'-Monophosphate Decarboxylase, 3-Deazauridine 5'-Monophosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, V. Iiams, J. A. Gerlt, S. C. Almo
Crystal Structure Of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed With 3-Deazauridine 5'-Monophosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRF, MTH_129
    Mutation: YES
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262
    Synonym: OMP DECARBOXYLASE, OMPDCASE, OMPDECASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
13DU2Ligand/Ion4-HYDROXY-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)PYRIDIN-2(1H)-ONE
2CA2Ligand/IonCALCIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , LYS A:42 , ASP A:70 , LYS A:72 , MET A:126 , SER A:127 , PRO A:180 , GLY A:202 , ARG A:203 , HOH A:419 , HOH A:434 , HOH A:435 , HOH A:448 , HOH A:452 , HOH A:453 , HOH A:460 , HOH A:472 , ASP B:75 , ILE B:76 , THR B:79BINDING SITE FOR RESIDUE 3DU A 301
2AC2SOFTWAREARG A:5 , VAL A:8 , ASP A:10 , HOH A:431 , HOH A:465BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREGLY A:52 , MET A:53 , ASP A:54 , HOH A:426 , GLY B:52 , MET B:53 , ASP B:54 , HOH B:421BINDING SITE FOR RESIDUE PEG A 303
4AC4SOFTWAREASP A:75 , THR A:79 , ASP B:20 , LYS B:42 , ASP B:70 , LYS B:72 , MET B:126 , SER B:127 , GLY B:202 , ARG B:203 , HOH B:413 , HOH B:423 , HOH B:426 , HOH B:446 , HOH B:448 , HOH B:450 , HOH B:457BINDING SITE FOR RESIDUE 3DU B 301
5AC5SOFTWAREARG B:5 , VAL B:8 , ASP B:10 , HOH B:463 , HOH B:465BINDING SITE FOR RESIDUE CA B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NT0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NT0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NT0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NT0)

(-) Exons   (0, 0)

(no "Exon" information available for 4NT0)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains d4nt0a_ A: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhh...eeee..hhhhh..eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt0 A   2 RSRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIK 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       190       200       210       220   
                                                                                                                                                                                                            180|                                 
                                                                                                                                                                                                             190                                 


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4nt0b_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eeeee...hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhh...eeee.hhhhhh..eeeehhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt0 B   2 RSRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIK 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       190       200       210       220   
                                                                                                                                                                                                            180|                                 
                                                                                                                                                                                                             190
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NT0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NT0)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    3DU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4nt0)
 

(-) 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
  4nt0
    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
  PYRF_METTH | O26232
    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)
  4.1.1.23
    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
  PYRF_METTH | O26232
    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
        PYRF_METTH | O26232: 1dv7 1dvj 1kly 1klz 1km0 1km1 1km2 1km3 1km4 1km5 1km6 1lol 1loq 1lor 1los 1lp6 1x1z 2e6y 2zz1 2zz2 2zz3 2zz4 2zz5 2zz6 2zz7 3g18 3g1a 3g1d 3g1f 3g1h 3g1s 3g1v 3g1x 3g1y 3g22 3g24 3lht 3lhu 3lhv 3lhw 3lhy 3lhz 3li0 3li1 3lld 3llf 3ltp 3lts 3lty 3lv5 3lv6 3m1z 3m41 3m43 3m44 3m47 3m5x 3m5y 3m5z 3nq6 3nq7 3nqa 3nqc 3nqd 3nqe 3nqf 3nqg 3nqm 3p5y 3p5z 3p60 3p61 3pbu 3pbv 3pbw 3pby 3pc0 3qez 3qf0 3qmr 3qms 3qmt 3rlu 3rlv 3sec 3sgu 3siz 3sj3 3ssj 3sw6 3sy5 3thq 3v1p 3w07 3wjw 3wjx 3wjy 3wjz 3wk0 3wk1 3wk2 3wk3 4fx6 4fx8 4fxr 4gc4 4lc6 4lc8 4lw7 4nuw 4nx5 4o11 4o8r

(-) Related Entries Specified in the PDB File

3g18 THE SAME PROTEIN UNCOMPLEXED