SMTL ID : 4ubs.1

The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 28 residues within 4Å: Chain A: L.83, L.84, H.91, R.95, I.147, L.228, L.229, A.232, G.233, T.236, T.237, M.240, L.273, A.279, L.282, R.284, A.334, F.335, G.336, I.339, H.340, Q.341, C.342, L.343, G.344, A.348, M.352 Ligands: DIF.3 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:L.83, A:L.84, A:I.147, A:L.228, A:A.232, A:M.240, A:L.273, A:A.279, A:F.335, A:F.335, A:L.343 Salt bridges: A:H.91, A:R.95, A:R.284, A:H.340 Metal complexes: A:C.342

2 x DIF: 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID(Non-covalent)

DIF.2: 12 residues within 4Å: Chain A: R.61, V.76, L.84, L.168, R.181, S.224, T.227, L.228, I.231 Ligands: DIF.3, PGE.4, PO4.23 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.84, A:L.168, A:T.227, A:L.228 Hydrogen bonds: A:R.181 Salt bridges: A:R.61 Halogen bonds: A:R.61 DIF.3: 13 residues within 4Å: Chain A: L.84, T.236, A.279, D.280, G.281, L.282, L.283, R.284, I.383 Ligands: HEM.1, DIF.2, PGE.4, PO4.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.236, A:A.279, A:I.383 Hydrogen bonds: A:L.283 Salt bridges: A:R.284

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 8 residues within 4Å: Chain A: R.72, F.73, L.168, L.169, V.177, D.381 Ligands: DIF.2, DIF.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.69, A:R.72, A:R.72, A:D.381 PGE.5: 2 residues within 4Å: Chain A: Y.189, R.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.219 PGE.6: 6 residues within 4Å: Chain A: S.163, R.166, R.167, R.170, G.171, P.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.166 PGE.7: 5 residues within 4Å: Chain A: D.119, L.122, D.123, E.126, R.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126, A:E.126, A:R.362 Water bridges: A:D.119 PGE.8: 8 residues within 4Å: Chain A: A.124, M.125, Q.128, S.136, A.137, P.141, M.145, Y.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.124, A:Y.155 Water bridges: A:M.125

14 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 5 residues within 4Å: Chain A: E.116, T.117, G.120, L.121, M.145 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.116 PEG.10: 2 residues within 4Å: Chain A: A.260, E.261 No protein-ligand interaction detected (PLIP) PEG.11: 1 residues within 4Å: Chain A: R.330 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.270 PEG.12: 2 residues within 4Å: Chain A: T.78 Ligands: PEG.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.75 PEG.13: 2 residues within 4Å: Chain A: I.174, Q.178 No protein-ligand interaction detected (PLIP) PEG.14: 6 residues within 4Å: Chain A: R.250, R.367, L.368, A.370, P.371, A.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.372 PEG.15: 4 residues within 4Å: Chain A: E.353, G.357, T.358, E.361 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.111 PEG.16: 5 residues within 4Å: Chain A: T.62, E.74, R.77, T.78 Ligands: PEG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.62 PEG.17: 2 residues within 4Å: Chain A: A.156, D.157 No protein-ligand interaction detected (PLIP) PEG.18: 5 residues within 4Å: Chain A: Q.128, P.131, A.132, E.133, P.390 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.133 PEG.19: 2 residues within 4Å: Chain A: R.196, R.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.196, A:R.196 PEG.20: 4 residues within 4Å: Chain A: E.261, P.262, G.263, L.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.261, A:G.263 PEG.21: 3 residues within 4Å: Chain A: D.157, F.160, Y.187 No protein-ligand interaction detected (PLIP) PEG.22: 2 residues within 4Å: Chain A: P.172, G.173 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.23: 9 residues within 4Å: Chain A: S.59, R.61, F.66, F.73, V.81, L.84, G.85 Ligands: DIF.2, DIF.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.61, A:L.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, L.H. et al., Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase. Appl.Microbiol.Biotechnol. (2015)

Release Date

2014-11-05

Peptides

Pentalenic acid synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pentalenic acid synthase