Structure of PDB 5dqn Chain A Binding Site BS01

Receptor Information
>5dqn Chain A (length=410) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTPNIPSDFDFLDATLNLERLPVEELAELRKSEPIHWVDVPGGTGGFGDK
GYWLVTKHADVKEVSRRSDVFGSSPDGAIPVYPQDMTREAVDLQRAVLLN
MDAPQHTRLRKIISRGFTPRAIGRLEDELRSRAQKIAQTAAAQGAGDFVE
QVSCELPLQAIAELLGVPQDDRDKLFRWSNEMTAGEDPEYADVDPAMSSF
ELISYAMKMAEERAVNPTEDIVTKLIEADIDGEKLSDDEFGFFVVMLAVA
GNETTRNSITHGMIAFAQNPDQWELYKKERPETAADEIVRWATPVSAFQR
TALEDVELGGVQIKKGQRVVMSYRSANFDEEVFEDPHTFNILRSPNPHVG
FGGTGAHYCIGANLARMTINLIFNAIADNMPDLKPIGAPERLKSGWLNGI
KHWQVDYTGA
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 chain5dqn Chain A Residue 501 [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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PDB5dqn Cytochrome P450 125A4, the Third Cholesterol C-26 Hydroxylase from Mycobacterium smegmatis.
Resolution2.262 Å
Binding residue
(original residue number in PDB)		L99 H107 R111 F118 L248 A251 G252 T255 T256 P295 G351 F352 G353 H358 Y359 C360 I361 G362 A366
Binding residue
(residue number reindexed from 1)		L98 H106 R110 F117 L247 A250 G251 T254 T255 P294 G350 F351 G352 H357 Y358 C359 I360 G361 A365
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) A185 A251 E254 T255 T256 C360 I361 G362 T369 L398
Catalytic site (residue number reindexed from 1) A184 A250 E253 T254 T255 C359 I360 G361 T368 L397
Enzyme Commision number 1.14.15.29: cholest-4-en-3-one 26-monooxygenase [(25S)-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:5dqn, PDBe:5dqn, PDBj:5dqn
PDBsum5dqn
PubMed26522442
UniProtA0R4Y3|CP125_MYCS2 Steroid C26-monooxygenase (Gene Name=cyp125)

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