Structure of PDB 2d09 Chain A Binding Site BS01

Receptor Information

>2d09 Chain A (length=404) Species: 100226 (Streptomyces coelicolor A3(2))

ETISQAVPPVRDWPAVDLPGSDFDPVLTELMREGPVTRISLPNGEGWAWL
VTRHDDVRLVTNDPRFGREAVMDRQVTRLAPHFIPARGAVGFLDPPDHTR
LRRSVAAAFTARGVERVRERSRGMLDELVDAMLRAGPPADLTEAVLSPFP
IAVICELMGVPATDRHSMHTWTQLILSSSHGAEVSERAKNEMNAYFSDLI
GLRSDSAGEDVTSLLGAAVGRDEITLSEAVGLAVLLQIGGEAVTNNSGQM
FHLLLSRPELAERLRSEPEIRPRAIDELLRWIPHRNAVGLSRIALEDVEI
KGVRIRAGDAVYVSYLAANRDPEVFPDPDRIDFERSPNPHVSFGFGPHYC
PGGMLARLESELLVDAVLDRVPGLKLAVAPEDVPFKKGALIRGPEALPVT
WAAA

Ligand information

• Ligand ID: HEM
• InChI: InChI=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-;
• InChIKey: KABFMIBPWCXCRK-RGGAHWMASA-L
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1c2n3c(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 3.385: CC1=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 12.01: C=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
• Formula: C34 H32 Fe N4 O4
• Name: PROTOPORPHYRIN IX CONTAINING FE;
  HEME
• DrugBank: DB18267
• PDB chain: 2d09 Chain A Residue 430

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2d09 Role of active site water molecules and substrate hydroxyl groups in oxygen activation by cytochrome P450 158A2: a new mechanism of proton transfer
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): R71 V93 H101 R105 L239 G242 G243 H287 R295 Y318 S345 F346 H351 C353 P354 G355 A359
• Binding residue (residue number reindexed from 1): R68 V90 H98 R102 L236 G239 G240 H284 R292 Y315 S342 F343 H348 C350 P351 G352 A356
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S180 G242 E244 A245 V246 N289 C353 P354 G355 E362 I394
• Catalytic site (residue number reindexed from 1): S177 G239 E241 A242 V243 N286 C350 P351 G352 E359 I391
• Enzyme Commision number: 1.14.19.69: biflaviolin 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:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0042440 pigment metabolic process

External links

• PDB: RCSB:2d09, PDBe:2d09, PDBj:2d09
• PDBsum: 2d09
• PubMed: 16239228
• UniProt: Q9FCA6|C1582_STRCO Biflaviolin synthase CYP158A2 (Gene Name=cyp158a2)