SMTL ID : 8dme.1

CYP102A1 in Open Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: K.67, L.73, L.84, F.85, W.94, F.105, I.151, F.259, A.262, G.263, T.266, T.267, T.325, A.326, F.329, P.390, F.391, G.392, R.396, A.397, C.398, I.399, G.400, F.403, A.404 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:L.84, A:F.85, A:F.85, A:F.85, A:F.105, A:I.151, A:F.259, A:F.259, A:A.262, A:F.391, A:I.399, A:F.403 Salt bridges: A:K.67, A:R.396 Metal complexes: A:C.398 HEM.10: 25 residues within 4Å: Chain B: K.67, L.73, L.84, F.85, W.94, F.105, I.151, F.259, A.262, G.263, T.266, T.267, T.325, A.326, F.329, P.390, F.391, G.392, R.396, A.397, C.398, I.399, G.400, F.403, A.404 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:F.85, B:F.85, B:F.85, B:F.105, B:I.151, B:F.259, B:F.259, B:A.262, B:F.391, B:I.399, B:F.403 Salt bridges: B:K.67, B:R.396 Metal complexes: B:C.398

2 x 1C6: 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole(Non-covalent)

1C6.2: 12 residues within 4Å: Chain A: V.24, Y.49, A.72, F.85, L.186, I.261, A.262, A.326, P.327, A.328, L.435, T.436 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.24, A:A.72, A:F.85, A:L.186, A:A.262, A:L.435 Hydrogen bonds: A:A.328 pi-Stacking: A:F.85 1C6.11: 12 residues within 4Å: Chain B: V.24, Y.49, A.72, F.85, L.186, I.261, A.262, A.326, P.327, A.328, L.435, T.436 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.24, B:A.72, B:F.85, B:L.186, B:A.262 Hydrogen bonds: B:Y.49, B:A.328 pi-Stacking: B:F.85

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 18 residues within 4Å: Chain A: S.474, N.475, M.476, G.477, T.478, A.479, A.520, S.521, Y.522, N.523, G.524, C.555, G.556, D.557, W.560, T.563, Y.564, Q.565 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.522, A:Y.522 Hydrogen bonds: A:N.475, A:M.476, A:G.477, A:T.478, A:T.478, A:T.478, A:A.479, A:S.521, A:S.521, A:Y.522, A:N.523, A:G.524, A:D.557, A:T.563, A:T.563, A:Q.565 pi-Stacking: A:W.560, A:W.560, A:W.560 FMN.12: 18 residues within 4Å: Chain B: S.474, N.475, M.476, G.477, T.478, A.479, A.520, S.521, Y.522, N.523, G.524, C.555, G.556, D.557, W.560, T.563, Y.564, Q.565 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.522, B:Y.522 Hydrogen bonds: B:N.475, B:M.476, B:G.477, B:T.478, B:T.478, B:T.478, B:A.479, B:S.521, B:S.521, B:N.523, B:G.524, B:D.557, B:T.563, B:T.563, B:Q.565 pi-Stacking: B:W.560, B:W.560, B:W.560

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.4: 22 residues within 4Å: Chain A: H.685, Q.742, R.783, R.813, Y.814, Y.815, S.816, T.831, V.832, S.833, V.835, E.838, A.839, W.840, Y.846, G.848, I.849, A.850, S.851, T.891, W.1032, G.1034 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.1032, A:W.1032 Hydrogen bonds: A:Q.742, A:Y.814, A:Y.814, A:Y.815, A:S.816, A:T.831, A:S.833, A:E.838, A:W.840, A:Y.846, A:I.849, A:A.850, A:S.851 Salt bridges: A:R.813, A:R.813 pi-Stacking: A:Y.815, A:W.840, A:W.840, A:W.840, A:Y.846, A:W.1032, A:W.1032 FAD.13: 22 residues within 4Å: Chain B: H.685, Q.742, R.783, R.813, Y.814, Y.815, S.816, T.831, V.832, S.833, V.835, E.838, A.839, W.840, Y.846, G.848, I.849, A.850, S.851, T.891, W.1032, G.1034 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.1032, B:W.1032 Hydrogen bonds: B:Q.742, B:Y.814, B:Y.814, B:S.816, B:T.831, B:S.833, B:E.838, B:W.840, B:I.849, B:A.850, B:S.851 Salt bridges: B:R.813, B:R.813 pi-Stacking: B:Y.815, B:W.840, B:W.840, B:W.840, B:Y.846, B:W.1032, B:W.1032

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

SO4.5: 5 residues within 4Å: Chain A: K.656, H.669, R.897, Y.931, E.934 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.656, A:H.669, A:R.897 SO4.6: 4 residues within 4Å: Chain A: R.923, S.951, R.952, Y.960 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.951, A:S.951 Salt bridges: A:R.952 SO4.7: 1 residues within 4Å: Chain A: R.665 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.665 SO4.14: 5 residues within 4Å: Chain B: K.656, H.669, R.897, Y.931, E.934 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.656, B:H.669, B:R.897 SO4.15: 4 residues within 4Å: Chain B: R.923, S.951, R.952, Y.960 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.951, B:Y.960 Salt bridges: B:R.952 SO4.16: 1 residues within 4Å: Chain B: R.665 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.665

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 7 residues within 4Å: Chain A: L.976, D.977, W.1017, Q.1020, L.1021, K.1024, R.1026 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.977, A:Q.1020, A:K.1024, A:R.1026 PG4.9: 5 residues within 4Å: Chain A: E.966, A.997, T.998, K.1001, S.1002 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.1002 PG4.17: 7 residues within 4Å: Chain B: L.976, D.977, W.1017, Q.1020, L.1021, K.1024, R.1026 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.1020, B:K.1024, B:R.1026 PG4.18: 5 residues within 4Å: Chain B: E.966, A.997, T.998, K.1001, S.1002 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.1002

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, M. et al., Insight into the conformational dynamics of cytochrome P450 CYP102A1 enzyme using Cryo-EM. To Be Published

Release Date

2023-07-19

Peptides

Bifunctional cytochrome P450/NADPH--P450 reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional cytochrome P450/NADPH--P450 reductase