Structure of PDB 2yoo Chain D Binding Site BS01

Receptor Information
>2yoo Chain D (length=394) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRPDVDLVNGMFYADGGAREAYRWMRANEPVFRDRNGLAAATTYQAVLDA
ERNPELFSSTGGIRPDQPGMPYMIDMDDPQHLLRRKLVNAGFTRKRVMDK
VDSIGRLCDTLIDAVCERGECDFVRDIAAPLPMAVIGDMLGVLPTERDML
LKWSDDLVCGLSSHVDEAAIQKLMDTFAAYTEFTKDVITKRRAEPTDDLF
SVLVNSEVEGQRMSDDEIVFETLLILIGGDETTRHTLSGGTEQLLRHRDQ
WDALVADVDLLPGAIEEMLRWTSPVKNMCRTLTADTVFHGTELRAGEKIM
LMFESANFDESVFGDPDNFRIDRNPNSHVAFGFGTHFCLGNQLARLELRL
MTERVLRRLPDLRLADDAPVPLRPANFVSGPESMPVVFTPSAPV
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 chain2yoo Chain D Residue 1402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2yoo A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		E56 I79 H86 R90 F97 G233 G234 T237 T238 V280 M283 R285 A335 F336 G337 F338 H341 C343 L344 G345
Binding residue
(residue number reindexed from 1)		E51 I74 H81 R85 F92 G228 G229 T232 T233 V275 M278 R280 A330 F331 G332 F333 H336 C338 L339 G340
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C164 G233 E236 T237 T238 C343 L344 G345 E352 V383
Catalytic site (residue number reindexed from 1) C159 G228 E231 T232 T233 C338 L339 G340 E347 V378
Enzyme Commision number 1.14.15.28: cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming].
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0008395 steroid hydroxylase activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 heme binding
GO:0036199 cholest-4-en-3-one 26-monooxygenase activity
GO:0046872 metal ion binding
Biological Process
GO:0006707 cholesterol catabolic process
GO:0008203 cholesterol metabolic process
GO:0016042 lipid catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2yoo, PDBe:2yoo, PDBj:2yoo
PDBsum2yoo
PubMed23489718
UniProtA0R4Q6|CP142_MYCS2 Steroid C26-monooxygenase (Gene Name=cyp142)

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