SMTL ID : 4ivm.2 (1 other biounit)

Structure of human protoporphyrinogen IX oxidase(R59G)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-dimer

Ligands

2 x ACJ: 5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID(Non-covalent)

ACJ.1: 17 residues within 4Å: Chain A: R.103, R.174, G.175, V.176, F.177, A.178, F.337, G.338, H.339, L.340, L.350, G.351, I.352, V.353, M.374, I.425 Ligands: FAD.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.340, A:L.340, A:V.353 Hydrogen bonds: A:G.338 Water bridges: A:R.68 Salt bridges: A:R.68, A:R.103 pi-Stacking: A:F.337 ACJ.5: 17 residues within 4Å: Chain B: R.103, R.174, G.175, V.176, F.177, A.178, F.337, G.338, H.339, L.340, L.350, G.351, I.352, V.353, M.374, I.425 Ligands: FAD.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.340, B:L.340, B:V.353 Hydrogen bonds: B:G.338 Water bridges: B:R.68 Salt bridges: B:R.68, B:R.103 pi-Stacking: B:F.337

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

FAD.2: 30 residues within 4Å: Chain A: G.15, G.16, G.17, I.18, S.19, V.39, E.40, S.41, G.47, W.48, I.49, L.62, G.63, P.64, G.65, G.66, P.262, V.263, A.291, I.292, V.296, V.322, I.425, G.454, A.455, V.460, A.461, V.462, C.465 Ligands: ACJ.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.322, A:I.425 Hydrogen bonds: A:G.15, A:G.16, A:I.18, A:S.19, A:S.19, A:S.19, A:S.41, A:S.41, A:G.47, A:W.48, A:G.65, A:G.66, A:V.263, A:V.263, A:A.455, A:V.462 Water bridges: A:G.17, A:G.20, A:S.42, A:I.49, A:I.49, A:S.456, A:N.463 FAD.6: 30 residues within 4Å: Chain B: G.15, G.16, G.17, I.18, S.19, V.39, E.40, S.41, G.47, W.48, I.49, L.62, G.63, P.64, G.65, G.66, P.262, V.263, A.291, I.292, V.296, V.322, I.425, G.454, A.455, V.460, A.461, V.462, C.465 Ligands: ACJ.5 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.322, B:I.425 Hydrogen bonds: B:G.15, B:G.16, B:I.18, B:S.19, B:S.19, B:S.19, B:S.41, B:S.41, B:G.47, B:W.48, B:G.65, B:G.66, B:V.263, B:V.263, B:A.455, B:V.462 Water bridges: B:G.17, B:G.20, B:S.42, B:I.49, B:I.49, B:S.456, B:N.463

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.431, Q.434, K.435, S.438 No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain A: R.187, S.188, W.433, L.436, R.440, E.458 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.187, A:R.440 GOL.7: 4 residues within 4Å: Chain B: G.431, Q.434, K.435, S.438 No protein-ligand interaction detected (PLIP) GOL.8: 6 residues within 4Å: Chain B: R.187, S.188, W.433, L.436, R.440, E.458 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.187, B:R.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Quantitative structural insight into human variegate porphyria disease. J.Biol.Chem. (2013)

Release Date

2013-03-06

Peptides

Protoporphyrinogen oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Protoporphyrinogen oxidase

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