Structure of PDB 8dme Chain A Binding Site BS03

Receptor Information

>8dme Chain A (length=1034) Species: 1348623 (Priestia megaterium NBRC 15308 = ATCC 14581)

KEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYL
SSQRLIKEACDESRFDKNLSQALKFVRDFFGDGLFTSWTHEKNWKKAHNI
LLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDT
IGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENK
RQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDE
NIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPV
PSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDE
LMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIG
QQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKK
IPLKKVRKKAENAHNTPLLVLYGSNMGTAEGTARDLADIAMSKGFAPQVA
TLDSHAGNLPREGAVLIVTASYNGHPPDNAKQFVDWLDQASADEVKGVRY
SVFGCGDKNWATTYQKVPAFIDETLAAKGAENIADRGEADASDDFEGTYE
EWREHMWSDVAAYFNLDIENSEDNKSTLSLQFVDSAADMPLAKMHGAFST
NVVASKELQQPGSARSTRHLEIELPKEASYQEGDHLGVIPRNYEGIVNRV
TARFGLDASQQIRLEAEEEKLAHLPLAKTVSVEELLQYVELQDPVTRTQL
RAMAAKTVCPPHKVELEALLEKQAYKEQVLAKRLTMLELLEKYPACEMKF
SEFIALLPSIRPRYYSISSSPRVDEKQASITVSVVSGEAWSGYGEYKGIA
SNYLAELQEGDTITCFISTPQSEFTLPKDPETPLIMVGPGTGVAPFRGFV
QARKQLKEQGQSLGEAHLYFGCRSPHEDYLYQEELENAQSEGIITLHTAF
SRMPNQPKTYVQHVMEQDGKKLIELLDQGAHFYICGDGSQMAPAVEATLM
KSYADVHQVSEADARLWLQQLEEKGRYAKDVWAG

Ligand information

• Ligand ID: FMN
• InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
• InChIKey: FVTCRASFADXXNN-SCRDCRAPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
  ACDLabs 12.01: N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
• Formula: C17 H21 N4 O9 P
• Name: FLAVIN MONONUCLEOTIDE;
  RIBOFLAVIN MONOPHOSPHATE
• ChEMBL: CHEMBL1201794
• DrugBank: DB03247
• ZINC: ZINC000003831425
• PDB chain: 8dme Chain A Residue 1103

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dme Insight into the conformational dynamics of cytochrome P450 CYP102A1 enzyme using Cryo-EM
• Resolution: 6.5 Å
• Binding residue (original residue number in PDB): S488 N489 M490 G491 T492 A493 A534 S535 Y536 N537 G570 D571 W574 T577 Y578
• Binding residue (residue number reindexed from 1): S474 N475 M476 G477 T478 A479 A520 S521 Y522 N523 G556 D557 W560 T563 Y564
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 1.14.14.1: unspecific monooxygenase.
  1.6.2.4: NADPH--hemoprotein reductase.

Gene Ontology

Molecular Function

• GO:0003958 NADPH-hemoprotein reductase activity
• GO:0004497 monooxygenase activity
• GO:0005506 iron ion binding
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
• GO:0016712 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
• GO:0020037 heme binding
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0070330 aromatase activity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:8dme, PDBe:8dme, PDBj:8dme
• PDBsum: 8dme
• UniProt: P14779|CPXB_PRIM2 Bifunctional cytochrome P450/NADPH--P450 reductase (Gene Name=cyp102A1)