Structure of PDB 8dme Chain B Binding Site BS04

Receptor Information

>8dme Chain B (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: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 8dme Chain B Residue 1104

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): H699 R797 R827 Y828 Y829 S830 T845 V846 E852 A853 W854 Y860 G862 I863 A864 S865 T905 W1046 G1048
• Binding residue (residue number reindexed from 1): H685 R783 R813 Y814 Y815 S816 T831 V832 E838 A839 W840 Y846 G848 I849 A850 S851 T891 W1032 G1034
• 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)