SMTL ID : 6laa.1

Crystal structure of full-length CYP116B46 from Tepidiphilus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

monomer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: F.80, L.117, V.118, H.125, R.129, F.136, M.267, A.275, T.278, T.279, P.320, V.321, W.324, R.326, N.377, F.378, G.379, Y.380, H.383, Q.384, C.385, L.386, G.387, G.391 Ligands: IMD.4, CO3.5 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.117, A:V.118, A:F.136, A:A.275, A:P.320, A:V.321, A:F.378, A:L.386 Hydrogen bonds: A:Y.380 Water bridges: A:R.326, A:H.383, A:H.383 Salt bridges: A:H.125, A:R.129, A:R.326, A:H.383 Metal complexes: A:C.385

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 10 residues within 4Å: Chain A: S.726, D.727, C.728, E.729, G.731, L.732, C.733, G.734, C.736, C.766 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.728, A:C.733, A:C.736, A:C.766

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 18 residues within 4Å: Chain A: R.513, Q.514, Y.515, S.516, A.530, V.531, Q.532, S.537, R.538, G.539, G.540, S.541, I.579, T.582, E.677, H.678, F.679, L.732 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Q.514, A:F.679 Hydrogen bonds: A:Q.514, A:Q.514, A:Y.515, A:S.516, A:A.530, A:Q.532, A:R.538, A:R.538, A:G.539, A:G.540, A:S.541, A:T.582 Water bridges: A:R.513, A:Q.514, A:D.534, A:A.536, A:F.679 Salt bridges: A:R.513, A:R.538 pi-Stacking: A:Y.515, A:F.679

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 4 residues within 4Å: Chain A: A.274, T.278, F.424 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.5: 6 residues within 4Å: Chain A: T.116, L.117, V.118, M.267, A.270 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

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

EDO.6: 8 residues within 4Å: Chain A: D.45, P.46, A.47, Y.317, N.318, A.350, H.354, R.425 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.45, A:D.45, A:A.47 Water bridges: A:Y.317, A:G.319 EDO.7: 5 residues within 4Å: Chain A: L.411, A.412, E.413, Q.414, F.416 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.414, A:Q.414 EDO.8: 5 residues within 4Å: Chain A: T.295, F.364, R.487, R.491, P.492 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.293, A:V.296, A:E.299, A:R.487 EDO.9: 6 residues within 4Å: Chain A: S.684, H.685, L.686, E.729, C.766, C.767 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.686 Water bridges: A:S.684 EDO.10: 7 residues within 4Å: Chain A: R.692, P.693, F.694, A.770, K.771, T.772, E.773 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.692, A:R.692 Water bridges: A:K.771 EDO.11: 7 residues within 4Å: Chain A: L.92, Y.111, F.113, H.201, N.204, A.205, Q.269 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.111, A:H.201, A:H.201, A:N.204, A:Q.269 EDO.12: 3 residues within 4Å: Chain A: Q.438, P.440, R.443 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.438, A:P.440, A:R.443, A:R.443, A:R.443 EDO.13: 6 residues within 4Å: Chain A: R.149, R.153, E.400, E.401, R.404, L.450 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.149, A:R.149, A:R.153 EDO.14: 6 residues within 4Å: Chain A: E.505, G.507, E.508, L.553, L.554, R.555 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.507, A:G.507, A:R.555, A:R.555 EDO.15: 4 residues within 4Å: Chain A: Q.532, G.578, I.579, F.680 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.532, A:I.579 Water bridges: A:Q.532 EDO.16: 9 residues within 4Å: Chain A: Y.73, K.77, S.373, E.374, H.375, G.379, Y.380, Q.384, E.723 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.73, A:Y.73, A:K.77, A:Q.384, A:E.723, A:E.723 EDO.17: 4 residues within 4Å: Chain A: N.157, R.405, E.441, L.448 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.157 Water bridges: A:N.157 EDO.18: 2 residues within 4Å: Chain A: R.191, R.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.195 EDO.19: 3 residues within 4Å: Chain A: H.625, V.626, Y.627 No protein-ligand interaction detected (PLIP) EDO.20: 7 residues within 4Å: Chain A: A.576, H.601, Y.602, S.603, N.635, L.637, M.658 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.601, A:S.603, A:N.635

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L.L. et al., Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase. Nat Commun (2020)

Release Date

2020-06-10

Peptides

Cytochrome P450: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome P450