SMTL ID : 6jlv.2 (1 other biounit)

Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

monomer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: K.70, L.76, L.87, F.88, W.97, F.262, A.265, G.266, T.269, T.270, L.323, 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 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.87, A:F.88, A:A.265, A:T.269, A:L.323, A:F.394, A:I.402, A:F.406 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, H2O.1

1 x WAA: (2S)-2-[[(1R,4aR,4bR,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,4b,5,6,10,10a-octahydrophenanthren-1-yl]carbonylamino]-3-( 1H-indol-3-yl)propanoic acid(Non-covalent)

WAA.2: 17 residues within 4Å: Chain A: L.21, P.26, V.27, L.30, R.48, Y.52, S.73, Q.74, A.75, L.76, V.79, F.88, M.186, L.189, A.331, M.355, L.438 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.26, A:V.27, A:L.30, A:Q.74, A:Q.74, A:A.75, A:L.76, A:V.79, A:F.88, A:A.331, A:L.438, A:L.438 Hydrogen bonds: A:R.48, A:Y.52, A:Q.74, A:A.75, A:L.189 pi-Cation interactions: A:R.48

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: E.132, R.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.129, A:R.133 Water bridges: A:E.132, A:E.132 GOL.4: 5 residues within 4Å: Chain A: I.367, R.379, A.385, I.386, P.387 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.367, A:R.379 Water bridges: A:R.376, A:R.376 GOL.5: 7 residues within 4Å: Chain A: K.392, F.394, G.395, N.396, G.397, A.400, Q.404 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.392, A:G.397, A:Q.404, A:Q.404 Water bridges: A:H.389, A:F.391, A:F.394 GOL.6: 3 residues within 4Å: Chain A: E.138, H.139, E.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.139, A:E.141 Water bridges: A:E.141 GOL.7: 3 residues within 4Å: Chain A: H.286, Q.289, K.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.286, A:K.290, A:K.290 GOL.8: 6 residues within 4Å: Chain A: V.282, P.285, L.288, F.424, E.425, D.426 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.282, A:D.426 Water bridges: A:F.424, A:F.424 GOL.9: 5 residues within 4Å: Chain A: N.320, F.380, P.383, I.386, F.391 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: D.69, T.92, H.93, K.337 Ligands: GOL.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.92, A:K.337 Water bridges: A:E.65, A:D.69, A:Q.398, A:Q.398 GOL.11: 4 residues within 4Å: Chain A: T.92, K.98, Q.398 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.98, A:Q.398, A:Q.398

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 8 residues within 4Å: Chain A: W.131, E.132, L.134, N.135, A.136, A.449, K.450, S.451 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.132, A:L.134, A:N.135, A:S.451 Water bridges: A:E.132, A:A.449, A:K.450, A:S.451

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanfield, J.K. et al., Crystals in Minutes: Instant On-Site Microcrystallisation of Various Flavours of the CYP102A1 (P450BM3) Haem Domain. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2020-03-18

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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