Structure of PDB 3nc3 Chain B Binding Site BS01

Receptor Information
>3nc3 Chain B (length=385) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKLFSVLSDQFQNNPYAYFSQLREEDPVHYEESIDSYFISRYHDVRYILQ
HPDIFTTKSLVERAEPVMRGPSAKRRIVVRSFIGDALDHLSPLIKQNAEN
LLAPYLERGKSDLVNDFGKTFAVCVTMDMLGLDKRDHEKISEWHSGVADF
ITSISQSPEARAHSLWCSEQLSQYLMPVIKERRVNPGSDLISILCTSALS
DKDILALILNVLLAATEPADKTLALMIYHLLNNPEQMNDVLADRSLVPRA
IAETLRYKPPVQLIPRQLSQDTVVGGMEIKKDTIVFCMIGAANRDPEAFE
QPDVFNIHREDLGIKSAFSGAARHLAFGSGIHNCVGTAFAKNEIEIVANI
VLDKMRNIRLEEDFCYAESGLYTRGPVSLLVAFDG
Ligand information
Ligand IDHEM
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain3nc3 Chain B Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nc3 Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase.
Resolution2.66 Å
Binding residue
(original residue number in PDB)		S63 M143 N229 A233 A234 P237 V280 I283 A345 F346 H351 C353 V354 G355 F358 A359
Binding residue
(residue number reindexed from 1)		S59 M129 N210 A214 A215 P218 V261 I264 A326 F327 H332 C334 V335 G336 F339 A340
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D163 A233 E236 P237 A238 C353 V354 G355 E362 T392
Catalytic site (residue number reindexed from 1) D149 A214 E217 P218 A219 C334 V335 G336 E343 T373
Enzyme Commision number 1.14.15.13: pulcherriminic acid synthase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0016713 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0046148 pigment biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:3nc3, PDBe:3nc3, PDBj:3nc3
PDBsum3nc3
PubMed20690619
UniProtO34926|CYPX_BACSU Pulcherriminic acid synthase (Gene Name=cypX)

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