SMTL ID : 7d1f.1 (1 other biounit)

Structure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-phenylalanine in complex with Methylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 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, 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: NME.3 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.87, A:F.88, A:F.88, A:F.88, A:F.108, A:I.154, A:F.262, A:A.265, A:L.273, A:F.394, A:I.402 Hydrogen bonds: A:R.399 Water bridges: A:K.70, A:K.70, A:H.101, A:S.333, A:S.333, A:S.333 Salt bridges: A:K.70, A:R.399 Metal complexes: A:C.401

1 x D0L: (2S)-2-[[(2S)-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid(Non-covalent)

D0L.2: 19 residues within 4Å: Chain A: L.21, P.26, L.30, F.43, A.45, R.48, Y.52, S.73, Q.74, A.75, F.88, M.186, L.189, A.329, P.330, A.331, M.355, L.438 Ligands: NME.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.21, A:P.26, A:L.30, A:F.43, A:A.45, A:R.48, A:A.75, A:F.88, A:A.329, A:L.438 Hydrogen bonds: A:Q.74, A:A.75 Salt bridges: A:R.48 pi-Cation interactions: A:R.48

1 x NME: METHYLAMINE(Non-covalent)

NME.3: 5 residues within 4Å: Chain A: F.88, A.265, T.269 Ligands: HEM.1, D0L.2 No protein-ligand interaction detected (PLIP)

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: T.23, D.24, P.26, M.186, N.187, Q.190, E.436, T.437 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.23, A:Q.190 Water bridges: A:E.436, A:T.437 GOL.5: 7 residues within 4Å: Chain A: W.131, L.134, N.135, A.136, A.449, K.450, S.451 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.131, A:N.135, A:S.451 Water bridges: A:S.451 GOL.6: 6 residues within 4Å: Chain A: V.309, K.310, L.312, K.313, G.316, T.412 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.310, A:K.310, A:L.312, A:T.412 GOL.7: 7 residues within 4Å: Chain A: K.392, F.394, G.395, N.396, G.397, A.400, Q.404 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.392, A:K.392, A:G.397, A:Q.404, A:Q.404 Water bridges: A:H.389, A:N.396, A:N.396 GOL.8: 5 residues within 4Å: Chain A: T.23, K.25, Q.28, A.29, K.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.23, A:K.25 GOL.9: 4 residues within 4Å: Chain A: D.69, T.92, H.93, K.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.69, A:K.337 Water bridges: A:D.69 GOL.10: 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.11: 4 residues within 4Å: Chain A: R.80, G.84, D.85, E.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.80, A:E.253 Water bridges: A:R.80, A:N.96 GOL.12: 2 residues within 4Å: Chain A: K.10, F.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.10, A:K.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shoji, O. et al., Structure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-phenylalanine in complex with Methylamine at 1.45 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
A

Bifunctional cytochrome P450/NADPH--P450 reductase

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