3C86 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   OPDA FROM AGROBACTERIUM RADIOBACTER WITH BOUND PRODUCT DIETHYL THIOPHOSPHATE FROM CRYSTAL SOAKING 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 :   10 Feb 08 (Deposition) - 19 Feb 08 (Release) - 07 Jul 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)

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 5)

No.	Name	Count	Type	Full Name
1	CO	1	Ligand/Ion	COBALT (II) ION
2	DPJ	1	Ligand/Ion	O,O-DIETHYL HYDROGEN THIOPHOSPHATE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	FE2	1	Ligand/Ion	FE (II) ION
5	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	DPJ	1	Ligand/Ion	O,O-DIETHYL HYDROGEN THIOPHOSPHATE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	FE2	1	Ligand/Ion	FE (II) ION
5	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 2 (4, 8)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	DPJ	2	Ligand/Ion	O,O-DIETHYL HYDROGEN THIOPHOSPHATE
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	FE2	2	Ligand/Ion	FE (II) ION
5	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DPJ A:1 , HIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , CO A:801 , HOH A:1085	BINDING SITE FOR RESIDUE FE2 A 800
2	AC2	SOFTWARE	DPJ A:1 , KCX A:169 , HIS A:201 , HIS A:230 , ARG A:254 , FE2 A:800 , HOH A:1085	BINDING SITE FOR RESIDUE CO A 801
3	AC3	SOFTWARE	HIS A:57 , GLY A:60 , TRP A:131 , KCX A:169 , HIS A:201 , ARG A:254 , TYR A:257 , ASP A:301 , LEU A:303 , EDO A:701 , FE2 A:800 , CO A:801 , HOH A:1085	BINDING SITE FOR RESIDUE DPJ A 1
4	AC4	SOFTWARE	DPJ A:1 , SER A:308	BINDING SITE FOR RESIDUE EDO A 701

(no "SS Bond" information available for 3C86)

(no "Cis Peptide Bond" information available for 3C86)

(no "SAP(SNP)/Variant" information available for 3C86)

(no "PROSITE Motif" information available for 3C86)

(no "Exon" information available for 3C86)

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
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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 d3c86a_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3c86A00 A:34-361 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 3c86 A  34 GDLINTVRGPIPVSEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRHARAAGVQTIVDVSTFDIGRDVRLLAEVSRAADVHIVAATGLWFDPPLSMRMRSVEELTQFFLREIQHGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTSASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTGLAARGYLVGLDRMPYSAIGLEGNASALALFGTRSWQTRALLIKALIDRGYKDRILVSHDWLFGFSSYVTNIMDVMDRINPDGMAFVPLRVIPFLREKGVPPETLAGVTVANPARFLSPT 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)
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	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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Metallo-dependent hydrolases (273)

Family: Phosphotriesterase-like (43)

Protein domain: Phosphotriesterase (parathion hydrolase, PTE) (39)

Agrobacterium tumefaciens [TaxId: 358] (13)

d3c86a_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Metal-dependent hydrolases (190)

Agrobacterium tumefaciens. Organism_taxid: 358. (9)

3c86A00

A:34-361

(no "Pfam Domain" information available for 3C86)

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.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3c86)

Biological Units
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	3c86
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	Q93LD7_RHIRD \| Q93LD7
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	3.1.8.1
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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)
2r1p	OPDA WITH BOUND DIETHYL THIOPHOSPHATE FROM CO- CRYSTALLISATION WITH TETRAETHYL DITHIOPYROPHOSPHATE

Description

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Ligands, Modified Residues, Ions (5, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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