Structure of PDB 3nc7 Chain A Binding Site BS01

Receptor Information
>3nc7 Chain A (length=379) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKLFSVLSDQFQNNPYAYFSQLREEDPVHYEESIDSYFISRYHDVRYILQ
HPDIFTTKSLVERAEPVAKRRIVVRSFIGDALDHLSPLIKQNAENLLAPY
LERGKSDLVNDFGKTFAVCVTMDMLGLDKRDHEKISEWHSGVADFITSIS
QSPEARAHSLWCSEQLSQYLMPVIKERRVNPGSDLISILCTSALSDKDIL
ALILNVLLAATEPADKTLALMIYHLLNNPEQMNDVLADRSLVPRAIAETL
RYKPPVQLIPRQLSQDTVVGGMEIKKDTIVFCMIGAANRDPEAFEQPDVF
NIHREDLGIKSAFSGAARHLAFGSGIHNCVGTAFAKNEIEIVANIVLDKM
RNIRLEEDFCYAESGLYTRGPVSLLVAFD
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 chain3nc7 Chain A Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nc7 Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		L64 N229 A233 A234 P237 I283 R285 A345 F346 H351 C353 V354 F358
Binding residue
(residue number reindexed from 1)		L60 N205 A209 A210 P213 I259 R261 A321 F322 H327 C329 V330 F334
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) D144 A209 E212 P213 A214 C329 V330 G331 E338 T368
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:3nc7, PDBe:3nc7, PDBj:3nc7
PDBsum3nc7
PubMed20690619
UniProtO34926|CYPX_BACSU Pulcherriminic acid synthase (Gene Name=cypX)

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