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 :  OPDA FROM AGROBACTERIUM RADIOBACTER WITH BOUND PRODUCT DIETHYL THIOPHOSPHATE FROM CO-CRYSTALLISATION WITH TETRAETHYL DITHIOPYROPHOSPHATE- 1.8 A
 
Authors :  D. L. Ollis, C. J. Jackson, J. L. Foo, H. K. Kim, P. D. Carr, J. W. Liu, G. Salem
Date :  23 Aug 07  (Deposition) - 12 Feb 08  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Phosphotriesterase, Opda, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Jackson, J. L. Foo, H. K. Kim, P. D. Carr, J. W. Liu, G. Salem, D. L. Ollis
In Crystallo Capture Of A Michaelis Complex And Product-Binding Modes Of A Bacterial Phosphotriesterase
J. Mol. Biol. V. 375 1189 2008
PubMed-ID: 18082180  |  Reference-DOI: 10.1016/J.JMB.2007.10.061
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOTRIESTERASE
    Chains: A
    EC Number: 3.1.8.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCY76
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 33-360
    Gene: OPDA
    Mutation: YES
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358
    Synonym: PROTEIN OPDA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (5, 5)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2DPJ1Ligand/IonO,O-DIETHYL HYDROGEN THIOPHOSPHATE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4FE21Ligand/IonFE (II) ION
5KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2DPJ1Ligand/IonO,O-DIETHYL HYDROGEN THIOPHOSPHATE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4FE21Ligand/IonFE (II) ION
5KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2DPJ2Ligand/IonO,O-DIETHYL HYDROGEN THIOPHOSPHATE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4FE22Ligand/IonFE (II) ION
5KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDPJ A:1 , HIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , CO A:801BINDING SITE FOR RESIDUE FE2 A 800
2AC2SOFTWAREDPJ A:1 , KCX A:169 , HIS A:201 , HIS A:230 , FE2 A:800BINDING SITE FOR RESIDUE CO A 801
3AC3SOFTWAREHIS A:55 , HIS A:57 , TRP A:131 , KCX A:169 , HIS A:201 , HIS A:230 , ARG A:254 , TYR A:257 , LEU A:271 , ASP A:301 , EDO A:701 , FE2 A:800 , CO A:801BINDING SITE FOR RESIDUE DPJ A 1
4AC4SOFTWAREDPJ A:1 , TRP A:131 , SER A:308BINDING SITE FOR RESIDUE EDO A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R1P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R1P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R1P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R1P)

(-) Exons   (0, 0)

(no "Exon" information available for 2R1P)

(-) 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:328
 aligned with Q93LD7_RHIRD | Q93LD7 from UniProtKB/TrEMBL  Length:384

    Alignment length:328
                                    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        
         Q93LD7_RHIRD    33 GDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARSAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGNASALALFGTRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 360
               SCOP domains d2r1pa_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2r1pA00 A:34-361 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------PTE-2r1pA01 A:44-359                                                                                                                                                                                                                                                                                                        -- Pfam domains
         Sec.struct. author ..eeee..eeee.hhh..eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r1p A  34 GDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARAAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIkVATTGKATPFQELVLRAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGNASALALFGTRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 361
                                    43        53        63        73        83        93       103       113       123       133       143       153       163     | 173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        
                                                                                                                                                                 169-KCX
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q93LD7_RHIRD | Q93LD7)
molecular function
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009056    catabolic process    The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.

 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
    CO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DPJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    KCX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r1p)
 
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
  2r1p
    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
  Q93LD7_RHIRD | Q93LD7
    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)
  3.1.8.1
    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
  Q93LD7_RHIRD | Q93LD7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q93LD7_RHIRD | Q93LD7: 2d2g 2d2h 2d2j 2r1k 2r1l 2r1m 2r1n 3a3w 3a3x 3a4j 3c86 3ood 3oqe 3so7 3wml 4np7

(-) Related Entries Specified in the PDB File

2d2g OPDA WITH BOUND INHIBITOR DIMETHYL PHOSPHATE
2d2h OPDA WITH BOUND INHIBITOR TRIMETHYL PHOSPHATE
2d2j OPDA WITHOUT INHIBITOR/PRODUCT PRESENT
2r1k OPDA WITH BOUND DIETHYL PHOSPHATE FROM CRYSTAL SOAKING WITH THE COMPOUND
2r1l OPDA WITH BOUND DIETHYL THIOPHOSPHATE FROM CRYSTAL SOAKING WITH THE COMPOUND
2r1m OPDA WITH BOUND PRODUCT DIETHYL PHOSPHATE FROM CRYSTAL SOAKING WITH DIETHYL 4-METHOXYPHENYL PHOSPHATE (450H)
2r1n OPDA WITH BOUND SLOW SUBSTRATE DIETHYL 4-METHOXYPHENYL PHOSPHATE (20H)
2r1o OPDA WITH BOUND DIETHYL THIOPHOSPHATE FROM CRYSTAL SOAKING WITH TETRAETHYL DITHIOPYROPHOSPHATE