Structure of PDB 3pck Chain M Binding Site BS02

Receptor Information
>3pck Chain M (length=233) Species: 303 (Pseudomonas putida) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPN
FSHLGFGAHDHDLLLNFGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQAN
AGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGP
NDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQ
LIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFE
Ligand information
Ligand IDNNO
InChIInChI=1S/C6H5NO4/c8-5-2-1-4(6(9)10)3-7(5)11/h1-3,8H,(H,9,10)
InChIKeyPQTDJLRPWRPPLV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)c1ccc(O)[n+]([O-])c1
ACDLabs 10.04O=C(O)c1c[n+]([O-])c(O)cc1
OpenEye OEToolkits 1.5.0c1cc([n+](cc1C(=O)O)[O-])O
FormulaC6 H5 N O4
Name6-HYDROXYISONICOTINIC ACID N-OXIDE
ChEMBL
DrugBank
ZINC
PDB chain3pck Chain M Residue 550 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pck Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
Resolution2.13 Å
Binding residue
(original residue number in PDB)		Y324 Y408 W449 R457 H460 H462 I491
Binding residue
(residue number reindexed from 1)		Y24 Y105 W146 R154 H157 H159 I188
Annotation score2
Binding affinityMOAD: Kd=0.2uM
PDBbind-CN: -logKd/Ki=6.70,Kd=0.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y408 Y447 R457 H460 H462
Catalytic site (residue number reindexed from 1) Y105 Y144 R154 H157 H159
Enzyme Commision number 1.13.11.3: protocatechuate 3,4-dioxygenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005506 iron ion binding
GO:0008199 ferric iron binding
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0018578 protocatechuate 3,4-dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0009056 catabolic process
GO:0019619 3,4-dihydroxybenzoate catabolic process
GO:0042952 beta-ketoadipate pathway

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3pck, PDBe:3pck, PDBj:3pck
PDBsum3pck
PubMed9254600
UniProtP00437|PCXB_PSEPU Protocatechuate 3,4-dioxygenase beta chain (Gene Name=pcaH)

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