SMTL ID : 1sez.2 (1 other biounit)

Crystal Structure of Protoporphyrinogen IX Oxidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 30 residues within 4Å: Chain A: I.19, G.20, G.22, V.23, S.24, F.42, E.43, A.44, G.50, K.51, E.64, G.65, A.66, N.67, T.68, R.263, V.264, T.303, A.304, D.308, V.336, W.435, A.438, F.439, N.468, L.473, S.474, V.475, A.478 Ligands: OMN.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:K.51, A:V.336, A:A.438, A:F.439 Hydrogen bonds: A:S.24, A:A.44, A:E.45, A:K.51, A:N.67, A:T.68, A:T.68, A:R.263, A:V.264, A:V.264, A:N.468, A:V.475 Water bridges: A:V.23, A:E.45, A:E.45, A:L.52 Salt bridges: A:K.51 FAD.4: 31 residues within 4Å: Chain B: I.19, G.20, A.21, G.22, V.23, S.24, F.42, E.43, A.44, G.50, K.51, G.65, A.66, N.67, T.68, R.263, V.264, T.303, A.304, D.308, L.334, V.336, A.438, F.439, G.467, N.468, L.473, S.474, V.475, A.478 Ligands: OMN.5 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.334, B:V.336, B:A.438, B:F.439, B:F.439 Hydrogen bonds: B:A.21, B:S.24, B:A.44, B:K.51, B:N.67, B:T.68, B:T.68, B:R.263, B:V.264, B:V.264, B:N.468, B:V.475 Water bridges: B:G.50, B:L.52 Salt bridges: B:K.51 FAD.7: 30 residues within 4Å: Chain C: I.19, G.20, G.22, V.23, S.24, F.42, E.43, A.44, G.50, K.51, E.64, G.65, A.66, N.67, T.68, R.263, V.264, T.303, A.304, D.308, V.336, W.435, A.438, F.439, N.468, L.473, S.474, V.475, A.478 Ligands: OMN.8 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:K.51, C:V.336, C:A.438, C:F.439 Hydrogen bonds: C:S.24, C:A.44, C:E.45, C:K.51, C:N.67, C:T.68, C:T.68, C:R.263, C:V.264, C:V.264, C:D.308, C:N.468, C:V.475 Water bridges: C:V.23, C:E.45, C:E.45, C:L.52 Salt bridges: C:K.51 FAD.10: 31 residues within 4Å: Chain D: I.19, G.20, A.21, G.22, V.23, S.24, F.42, E.43, A.44, G.50, K.51, G.65, A.66, N.67, T.68, R.263, V.264, T.303, A.304, D.308, L.334, V.336, A.438, F.439, G.467, N.468, L.473, S.474, V.475, A.478 Ligands: OMN.11 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:L.334, D:V.336, D:A.438, D:F.439, D:F.439 Hydrogen bonds: D:A.21, D:S.24, D:A.44, D:K.51, D:N.67, D:T.68, D:T.68, D:R.263, D:V.264, D:V.264, D:D.308, D:N.468, D:V.475 Water bridges: D:G.50, D:L.52 Salt bridges: D:K.51

4 x OMN: 4-BROMO-3-(5'-CARBOXY-4'-CHLORO-2'-FLUOROPHENYL)-1-METHYL-5-TRIFLUOROMETHYL-PYRAZOL(Non-covalent)

OMN.2: 17 residues within 4Å: Chain A: R.98, A.174, G.175, C.177, G.178, L.334, F.353, G.354, V.355, L.356, L.369, G.370, T.371, L.372, F.392 Ligands: FAD.1, TON.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.356, A:L.372 Salt bridges: A:R.98 pi-Stacking: A:F.392 OMN.5: 17 residues within 4Å: Chain B: R.98, A.174, G.175, C.177, G.178, L.334, G.354, V.355, L.356, L.369, G.370, T.371, L.372, F.392, F.439 Ligands: FAD.4, TON.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.356, B:L.372 Salt bridges: B:R.98 pi-Stacking: B:F.392 OMN.8: 17 residues within 4Å: Chain C: R.98, A.174, G.175, C.177, G.178, L.334, F.353, G.354, V.355, L.356, L.369, G.370, T.371, L.372, F.392 Ligands: FAD.7, TON.9 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.356, C:L.372 Salt bridges: C:R.98 pi-Stacking: C:F.392 OMN.11: 17 residues within 4Å: Chain D: R.98, A.174, G.175, C.177, G.178, L.334, G.354, V.355, L.356, L.369, G.370, T.371, L.372, F.392, F.439 Ligands: FAD.10, TON.12 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.356, D:L.372 Salt bridges: D:R.98 pi-Stacking: D:F.392

4 x TON: 2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL(Non-covalent)

TON.3: 8 residues within 4Å: Chain A: R.98, L.109, L.168, I.169, F.172, L.193, L.356 Ligands: OMN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.172, A:F.172, A:F.172, A:L.193 TON.6: 8 residues within 4Å: Chain B: L.109, L.168, I.169, F.172, T.176, F.190, L.356 Ligands: OMN.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.172, B:F.172, B:F.190, B:F.190 TON.9: 8 residues within 4Å: Chain C: R.98, L.109, L.168, I.169, F.172, L.193, L.356 Ligands: OMN.8 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.172, C:F.172, C:F.172, C:L.193 TON.12: 8 residues within 4Å: Chain D: L.109, L.168, I.169, F.172, T.176, F.190, L.356 Ligands: OMN.11 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.172, D:F.172, D:F.190, D:F.190 Hydrogen bonds: D:T.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koch, M. et al., Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis. Embo J. (2004)

Release Date

2004-04-13

Peptides

Protoporphyrinogen oxidase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Protoporphyrinogen oxidase, mitochondrial

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