Structure of PDB 5l1o Chain A Binding Site BS02

Receptor Information
>5l1o Chain A (length=397) Species: 29301 (Streptomyces arenae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDLPRLPFDNPDIMGIAPQMLALQKEGPIARVGTAGEDAWLVTRYDEVRT
LLADRRLRLSNPNPQPSAKSAARAFMVALMAGDDHETEPARHAQMRSLLI
PRFSTRRLRLMKTRIEHHVDELLDQLAASAPPVDLHRVLSFRLPTMVVCD
LLGVPLADRERFGQWARGTFDQSDNEHSANTFQQVVDYMLELVARKRVEP
GDDILSELIAEKDGALSDADIAHLGNAVLLFGYETTIVRIDLGTLLLLRN
PVQRAQLAEDPGLAPAAVEEILRLGVGGKGSNALIPRYAHGDITVGETVI
RTGDAVMLAIGAANYDDRAFPDGGLFDLTRVRPRSHLAFGHGARHCIGRT
LARIELTAVFERLFRRLPDLRLAVPEESLRWQEHRITGGFDEIPVTF
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 chain5l1o Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5l1o The Cytochrome P450-Catalyzed Oxidative Rearrangement in the Final Step of Pentalenolactone Biosynthesis: Substrate Structure Determines Mechanism.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		M81 H93 R97 F104 G233 T236 T237 R240 I286 R288 A339 F340 R345 C347 G349
Binding residue
(residue number reindexed from 1)		M80 H92 R96 F103 G232 T235 T236 R239 I285 R287 A338 F339 R344 C346 G348
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D172 F232 E235 T236 T237 S282 C347 I348 G349 E356 T388
Catalytic site (residue number reindexed from 1) D171 F231 E234 T235 T236 S281 C346 I347 G348 E355 T387
Enzyme Commision number 1.14.19.8: pentalenolactone synthase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0016636 oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0017000 antibiotic biosynthetic process
GO:1901780 pentalenolactone biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5l1o, PDBe:5l1o, PDBj:5l1o
PDBsum5l1o
PubMed27588339
UniProtE3VWI3|PNTM_STRAE Pentalenolactone synthase (Gene Name=pntM)

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