Structure of PDB 3nc5 Chain B Binding Site BS01

Receptor Information
>3nc5 Chain B (length=373) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLFSVLSDQFQNNPYAYFSQLREEDPVHYEESIDSYFISRYHDVRYILQH
PDIFTTKSLVERARIVVRSFIGDALDHLSPLIKQNAENLLAPYLERGKSD
LVNDFGKTFAVCVTMDMLGLDKRDHEKISEWHSGVADFITSISQSPEARA
HSLWCSEQLSQYLMPVIKERRVNPGSDLISILCTSEALSDKDILALILNV
LLAATEPADKTLALMIYHLLNNPEQMNDVLADRSLVPRAIAETLRYKPPV
QLIPRQLSQDTVVGGMEIKKDTIVFCMIGAANRDPEAFEQPDVFNIHRED
LGIKSAFSGAARHLAFGSGIHNCVGTAFAKNEIEIVANIVLDKMRNIRLE
EDFCYAESGLYTRGPVSLLVAFD
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 chain3nc5 Chain B Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3nc5 Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		N229 A233 A234 P237 L274 I283 R285 A345 F346 H351 C353 G355
Binding residue
(residue number reindexed from 1)		N199 A203 A204 P207 L244 I253 R255 A315 F316 H321 C323 G325
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) D137 A203 E206 P207 A208 C323 V324 G325 E332 T362
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3nc5, PDBe:3nc5, PDBj:3nc5
PDBsum3nc5
PubMed20690619
UniProtO34926|CYPX_BACSU Pulcherriminic acid synthase (Gene Name=cypX)

[Back to BioLiP]