SMTL ID : 7cp8.2 (1 other biounit)

Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-1-Indanylamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: T.23, D.24, P.26, M.186, N.187, Q.190, E.436, T.437 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.190, A:E.436 Water bridges: A:T.437 GOL.2: 3 residues within 4Å: Chain A: E.138, H.139, E.141 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.139, A:H.139, A:E.141 Water bridges: A:K.130, A:E.141 GOL.3: 5 residues within 4Å: Chain A: I.367, W.368, R.379, A.385, I.386 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.367, A:R.379 GOL.4: 6 residues within 4Å: Chain A: H.101, G.397, Q.398, A.400, I.402 Ligands: HEM.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.398 GOL.5: 4 residues within 4Å: Chain A: D.69, T.92, H.93, K.337 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.337 Water bridges: A:E.65, A:D.69, A:T.92, A:Q.398 GOL.6: 7 residues within 4Å: Chain A: W.131, L.134, N.135, A.136, A.449, K.450, S.451 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.135, A:S.451 GOL.7: 5 residues within 4Å: Chain A: P.143, E.144, T.147, H.267, K.441 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.267, A:K.441 GOL.8: 5 residues within 4Å: Chain A: F.108, C.401, I.402, Q.404, Q.405 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.402, A:Q.404, A:Q.405 Water bridges: A:Q.405, A:Q.405 GOL.12: 2 residues within 4Å: Chain A: E.132, R.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.129, A:R.133 GOL.13: 5 residues within 4Å: Chain A: V.309, K.310, L.312, G.316, T.412 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.310, A:K.310, A:L.312 Water bridges: A:Q.110, A:G.316 GOL.14: 5 residues within 4Å: Chain A: R.80, G.84, D.85, E.253, Y.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.80, A:E.253

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

HEM.9: 25 residues within 4Å: Chain A: K.70, L.76, L.87, F.88, W.97, I.154, F.262, A.265, T.269, T.270, L.273, T.328, A.329, F.332, P.393, F.394, G.395, R.399, A.400, C.401, I.402, G.403, A.407 Ligands: GOL.4, RM1.10 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.87, A:F.88, A:F.88, A:I.154, A:F.262, A:F.262, A:A.265, A:L.273, A:T.328, A:A.329, A:F.394, A:I.402, A:A.407 Hydrogen bonds: A:R.399 Water bridges: A:K.70, A:K.70, A:S.333, A:S.333, A:S.333 Salt bridges: A:K.70, A:R.399 Metal complexes: A:C.401

1 x RM1: N-METHYL-1(R)-AMINOINDAN(Non-covalent)

RM1.10: 8 residues within 4Å: Chain A: F.88, I.264, A.265, A.329, L.438, T.439 Ligands: HEM.9, GKX.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.88, A:F.88, A:I.264, A:A.265, A:A.329, A:L.438, A:L.438, A:T.439 pi-Stacking: A:F.88

1 x GKX: (2~{S})-2-(5-cyclohexylpentanoylamino)-3-phenyl-propanoic acid(Non-covalent)

GKX.11: 16 residues within 4Å: Chain A: L.21, V.27, L.30, R.48, T.50, Y.52, S.73, Q.74, A.75, L.76, L.189, P.330, A.331, M.355, L.438 Ligands: RM1.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.21, A:Q.74, A:A.75, A:L.76, A:P.330, A:A.331, A:L.438 Hydrogen bonds: A:Y.52, A:Q.74, A:A.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shoji, O. et al., Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-1-Indanylamine at 1.68 Angstrom Resolution. To Be Published

Release Date

2021-09-15

Peptides

Bifunctional cytochrome P450/NADPH--P450 reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bifunctional cytochrome P450/NADPH--P450 reductase

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