SMTL ID : 3r9b.3 (2 other biounits)

Crystal structure of Mycobacterium smegmatis CYP164A2 in ligand free state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: F.97, L.98, H.105, R.109, F.116, I.159, L.252, L.253, A.256, G.257, T.260, T.261, L.264, M.297, P.302, V.303, V.306, R.308, G.358, F.359, G.360, A.363, H.364, C.366, L.367, G.368, A.372 Ligands: D12.13 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.97, A:F.97, A:F.116, A:I.159, A:L.252, A:L.253, A:A.256, A:T.260, A:L.264, A:P.302, A:V.306, A:A.372 Salt bridges: A:H.105, A:R.109, A:R.308, A:H.364 pi-Stacking: A:F.359 Metal complexes: A:C.366

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: E.235, L.241, T.242, E.243 Ligands: K.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.235, A:E.243 Water bridges: A:L.241, A:T.242, A:D.244 PO4.3: 4 residues within 4Å: Chain A: N.50, R.81 Ligands: EDO.7, NA.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.50 Water bridges: A:R.81, A:R.81 Salt bridges: A:R.81

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: A.183, D.185, F.187, L.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.187, A:L.188 Water bridges: A:A.189 EDO.5: 5 residues within 4Å: Chain A: H.105, R.109, G.362, A.363 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.362 EDO.6: 5 residues within 4Å: Chain A: V.341, G.342, R.351, A.352, Q.353 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.342, A:R.351, A:A.352, A:Q.353 EDO.7: 4 residues within 4Å: Chain A: P.47, E.48, R.81 Ligands: PO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.81 EDO.8: 4 residues within 4Å: Chain A: R.109, G.110, S.113 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.109, A:S.113 EDO.9: 7 residues within 4Å: Chain A: R.73, S.76, I.78, F.79, A.189, Y.309, T.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.76, A:T.326 Water bridges: A:A.189 EDO.10: 3 residues within 4Å: Chain A: S.56, D.59, G.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.56 Water bridges: A:S.58, A:D.59

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 1 residues within 4Å: Ligands: PO4.3 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.12: 4 residues within 4Å: Chain A: E.235, G.238, L.241 Ligands: PO4.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.235, A:G.238, A:L.241, H2O.2

1 x D12: DODECANE(Non-covalent)

D12.13: 9 residues within 4Å: Chain A: F.99, L.184, L.252, I.255, A.256, V.303, V.306, L.404 Ligands: HEM.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.99, A:L.184, A:L.252, A:I.255, A:I.255, A:A.256, A:V.303, A:V.306, A:L.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agnew, C.R. et al., An enlarged, adaptable active site in CYP164 family P450 enzymes, the sole P450 in Mycobacterium leprae. Antimicrob.Agents Chemother. (2012)

Release Date

2012-04-04

Peptides

CYTOCHROME P450 164A2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

CYTOCHROME P450 164A2

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