SMTL ID : 8dmg.1

CYP102A1 in Closed 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.70, L.76, L.87, F.88, W.97, F.108, I.154, F.262, A.265, G.266, T.269, T.270, T.328, A.329, F.332, P.393, F.394, G.395, R.399, A.400, C.401, I.402, G.403, F.406, A.407 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:F.88, A:F.88, A:F.88, A:F.108, A:I.154, A:F.262, A:F.262, A:A.265, A:F.394, A:I.402, A:F.406 Salt bridges: A:K.70, A:R.399 Metal complexes: A:C.401 HEM.10: 25 residues within 4Å: Chain B: K.70, L.76, L.87, F.88, W.97, F.108, I.154, F.262, A.265, G.266, T.269, T.270, T.328, A.329, F.332, P.393, F.394, G.395, R.399, A.400, C.401, I.402, G.403, F.406, A.407 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:F.88, B:F.88, B:F.88, B:F.108, B:I.154, B:F.262, B:F.262, B:A.265, B:F.394, B:I.402, B:F.406 Salt bridges: B:K.70, B:R.399 Metal complexes: B:C.401

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.27, Y.52, A.75, F.88, L.189, I.264, A.265, A.329, P.330, A.331, L.438, T.439 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.27, A:A.75, A:F.88, A:L.189, A:A.265 Hydrogen bonds: A:Y.52, A:A.331 pi-Stacking: A:F.88 1C6.11: 12 residues within 4Å: Chain B: V.27, Y.52, A.75, F.88, L.189, I.264, A.265, A.329, P.330, A.331, L.438, T.439 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.27, B:A.75, B:F.88, B:L.189, B:A.265 Hydrogen bonds: B:A.331 pi-Stacking: B:F.88

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 18 residues within 4Å: Chain A: S.477, N.478, M.479, G.480, T.481, A.482, A.523, S.524, Y.525, N.526, G.527, C.558, G.559, D.560, W.563, T.566, Y.567, Q.568 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.525, A:Y.525 Hydrogen bonds: A:N.478, A:M.479, A:G.480, A:T.481, A:T.481, A:T.481, A:A.482, A:S.524, A:S.524, A:Y.525, A:N.526, A:G.527, A:D.560, A:T.566, A:T.566, A:Q.568 pi-Stacking: A:W.563, A:W.563, A:W.563 FMN.12: 18 residues within 4Å: Chain B: S.477, N.478, M.479, G.480, T.481, A.482, A.523, S.524, Y.525, N.526, G.527, C.558, G.559, D.560, W.563, T.566, Y.567, Q.568 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.525, B:Y.525 Hydrogen bonds: B:N.478, B:M.479, B:G.480, B:T.481, B:T.481, B:T.481, B:A.482, B:S.524, B:S.524, B:N.526, B:G.527, B:D.560, B:T.566, B:T.566, B:Q.568 pi-Stacking: B:W.563, B:W.563, B:W.563

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

FAD.4: 22 residues within 4Å: Chain A: H.688, Q.745, R.786, R.816, Y.817, Y.818, S.819, T.834, V.835, S.836, V.838, E.841, A.842, W.843, Y.849, G.851, I.852, A.853, S.854, T.894, W.1035, G.1037 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.1035, A:W.1035 Hydrogen bonds: A:Q.745, A:Y.817, A:Y.817, A:S.819, A:T.834, A:S.836, A:E.841, A:W.843, A:I.852, A:A.853, A:S.854 Salt bridges: A:R.816, A:R.816 pi-Stacking: A:Y.818, A:W.843, A:W.843, A:W.843, A:Y.849, A:W.1035, A:W.1035 FAD.13: 22 residues within 4Å: Chain B: H.688, Q.745, R.786, R.816, Y.817, Y.818, S.819, T.834, V.835, S.836, V.838, E.841, A.842, W.843, Y.849, G.851, I.852, A.853, S.854, T.894, W.1035, G.1037 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:W.1035, B:W.1035 Hydrogen bonds: B:Q.745, B:Y.817, B:Y.817, B:Y.818, B:S.819, B:T.834, B:S.836, B:E.841, B:W.843, B:Y.849, B:I.852, B:A.853, B:S.854 Salt bridges: B:R.816, B:R.816 pi-Stacking: B:Y.818, B:W.843, B:W.843, B:W.843, B:Y.849, B:W.1035, B:W.1035

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

SO4.5: 5 residues within 4Å: Chain A: K.659, H.672, R.900, Y.934, E.937 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.659, A:H.672, A:R.900 SO4.6: 4 residues within 4Å: Chain A: R.926, S.954, R.955, Y.963 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.954, A:Y.963 Salt bridges: A:R.955 SO4.7: 1 residues within 4Å: Chain A: R.668 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.668 SO4.14: 5 residues within 4Å: Chain B: K.659, H.672, R.900, Y.934, E.937 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.659, B:H.672, B:R.900 SO4.15: 4 residues within 4Å: Chain B: R.926, S.954, R.955, Y.963 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.954, B:S.954 Salt bridges: B:R.955 SO4.16: 1 residues within 4Å: Chain B: R.668 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.668

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

PG4.8: 7 residues within 4Å: Chain A: L.979, D.980, W.1020, Q.1023, L.1024, K.1027, R.1029 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.1023, A:K.1027, A:R.1029 PG4.9: 5 residues within 4Å: Chain A: E.969, A.1000, T.1001, K.1004, S.1005 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.1005 PG4.17: 7 residues within 4Å: Chain B: L.979, D.980, W.1020, Q.1023, L.1024, K.1027, R.1029 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.980, B:Q.1023, B:K.1027, B:R.1029 PG4.18: 5 residues within 4Å: Chain B: E.969, A.1000, T.1001, K.1004, S.1005 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.1005

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