SMTL ID : 4aw3.1

Structure of the mixed-function P450 MycG F286V mutant in complex with mycinamicin V in P1 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: L.103, L.104, H.111, R.115, F.122, L.251, A.254, G.255, S.258, T.259, Q.262, L.300, A.305, V.306, R.308, G.358, F.359, G.360, V.363, H.364, C.366, L.367, G.368, A.372, E.375, L.376 Ligands: MYV.2 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.104, A:F.122, A:A.254, A:Q.262, A:L.300, A:F.359, A:F.359, A:L.367, A:L.376 Hydrogen bonds: A:V.306 Salt bridges: A:H.111, A:R.115, A:R.308, A:H.364 pi-Stacking: A:F.359 Metal complexes: A:C.366, H2O.7 HEM.9: 26 residues within 4Å: Chain B: L.103, L.104, H.111, R.115, F.122, L.251, A.254, G.255, S.258, T.259, Q.262, A.305, V.306, R.308, G.358, F.359, G.360, V.363, H.364, C.366, L.367, G.368, A.372, E.375, L.376 Ligands: MYV.10 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.122, B:Q.262, B:F.359, B:F.359, B:L.367, B:L.376 Hydrogen bonds: B:V.306 Salt bridges: B:H.111, B:R.115, B:R.308, B:H.364 Metal complexes: B:C.366, H2O.17

2 x MYV: MYCINAMICIN V(Non-covalent)

MYV.2: 12 residues within 4Å: Chain A: R.95, E.97, V.99, F.188, S.190, V.194, A.196, M.199, V.253, E.257, L.406 Ligands: HEM.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.97, A:F.188, A:E.257 Water bridges: A:R.95, A:R.95, A:V.253, A:E.257, A:E.257, A:E.257, A:E.257 MYV.10: 16 residues within 4Å: Chain B: R.95, E.97, V.99, G.101, G.102, L.103, L.104, F.188, S.190, V.194, M.199, V.253, A.254, E.257, L.406 Ligands: HEM.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.97, B:V.99, B:F.188, B:V.253, B:L.406, B:L.406 Hydrogen bonds: B:R.95, B:G.101, B:L.104 Water bridges: B:Y.256 Salt bridges: B:R.95

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: H.365, A.369, P.370, R.373 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.373 Salt bridges: A:H.365, A:R.373 SO4.4: 2 residues within 4Å: Chain A: R.115, V.119 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.115, A:V.363 Salt bridges: A:R.115 SO4.5: 3 residues within 4Å: Chain A: P.174, R.216, R.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.216 Salt bridges: A:R.217 SO4.6: 5 residues within 4Å: Chain A: A.40, G.41, R.42 Chain B: R.273, W.297 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.41, A:R.42 Salt bridges: A:R.42, B:R.273 Water bridges: B:R.273 SO4.11: 5 residues within 4Å: Chain A: T.38, R.273 Chain B: A.40, G.41, R.42 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Water bridges: A:L.37, A:T.38, A:T.38, A:R.273, A:R.273, A:R.273 Salt bridges: A:R.273, B:R.42 Hydrogen bonds: B:G.41, B:R.42 SO4.12: 5 residues within 4Å: Chain A: R.27 Chain B: R.273, P.274, E.275, L.276 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.275, B:L.276 Salt bridges: A:R.27 SO4.13: 4 residues within 4Å: Chain B: H.365, A.369, P.370, R.373 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.365, B:R.373 Salt bridges: B:H.365, B:R.373 SO4.14: 2 residues within 4Å: Chain B: R.115, V.119 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.115

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: Y.29, P.92, R.93, T.94, G.303, T.304 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.304, A:T.304 Water bridges: A:T.304, A:L.406 GOL.8: 8 residues within 4Å: Chain A: R.160, T.191, T.260, T.261, A.264, G.409, P.410, L.411 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.160, A:G.409 GOL.15: 6 residues within 4Å: Chain B: Y.29, P.92, R.93, T.94, G.303, T.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.304, B:T.304 Water bridges: B:G.303 GOL.16: 9 residues within 4Å: Chain B: R.160, T.191, T.260, T.261, A.264, S.402, G.409, P.410, L.411 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Substrate Recognition by the Multifunctional Cytochrome P450 Mycg in Mycinamicin Hydroxylation and Epoxidation Reactions. J.Biol.Chem. (2012)

Release Date

2012-09-05

Peptides

P-450-LIKE PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

P-450-LIKE PROTEIN