SMTL ID : 4l0f.1

Structure of P450sky (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis (open active site)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

HEM.1: 30 residues within 4Å: Chain A: Y.89, N.101, L.118, A.119, H.126, R.130, F.137, L.184, S.266, L.267, G.270, G.271, T.274, S.275, S.278, L.311, P.316, F.320, R.322, T.372, F.373, G.374, P.377, H.378, C.380, L.381, G.382, L.385, E.389 Ligands: PGE.16 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:A.119, A:F.137, A:L.184, A:L.311, A:P.316, A:F.320, A:F.320, A:T.372, A:F.373, A:L.381, A:L.381, A:L.385 Hydrogen bonds: A:N.101 Salt bridges: A:H.126, A:R.130, A:R.322, A:H.378 pi-Stacking: A:F.373 Metal complexes: A:C.380

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: H.20, F.286, T.287, P.290, W.293, G.403, F.404 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.404 EDO.3: 4 residues within 4Å: Chain A: A.356, D.357, D.362, R.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.362, A:R.365 Water bridges: A:S.366 EDO.4: 3 residues within 4Å: Chain A: E.352, V.354, A.356 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.352 EDO.5: 4 residues within 4Å: Chain A: P.144, I.145, Q.148, D.183 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: M.24, T.25, I.406, T.407, G.408 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.406 Water bridges: A:M.24 EDO.7: 1 residues within 4Å: Chain A: H.20 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: P.32, D.33, D.34, T.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.33, A:D.33, A:D.34 EDO.9: 4 residues within 4Å: Chain A: H.9, H.10, I.31, D.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.10, A:D.33 EDO.10: 6 residues within 4Å: Chain A: S.36, I.38, N.39, H.67, P.68, V.70 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: R.44, V.48 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.42 EDO.12: 4 residues within 4Å: Chain A: S.204, E.273, I.413, H.414 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.414, A:H.414 EDO.13: 3 residues within 4Å: Chain A: G.186, T.238, D.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.238, A:T.238 Water bridges: A:D.183 EDO.14: 5 residues within 4Å: Chain A: T.96, K.99, R.323, A.324, V.325 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.323 EDO.15: 3 residues within 4Å: Chain A: T.326, D.327, A.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.327, A:D.327 Water bridges: A:T.326

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

PGE.16: 9 residues within 4Å: Chain A: N.101, V.102, A.119, L.269, G.270, T.274, F.320, F.417 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.101 Water bridges: A:N.101, A:D.111, A:L.269, A:G.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uhlmann, S. et al., Cytochrome p450sky interacts directly with the nonribosomal Peptide synthetase to generate three amino Acid precursors in skyllamycin biosynthesis. Acs Chem.Biol. (2013)

Release Date

2013-09-25

Peptides

P450 monooxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

P450 monooxygenase

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