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

Structure of human protoporphyrinogen IX oxidase(R59Q)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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.68, 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 Ligands: FAD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.337, A:L.340, A:L.340, A:V.353 Hydrogen bonds: A:G.175, A:G.338 Water bridges: A:R.68, A:R.103 Salt bridges: A:R.68, A:R.103 ACJ.5: 17 residues within 4Å: Chain B: R.68, 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 Ligands: FAD.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.337, B:L.340, B:L.340, B:V.353 Hydrogen bonds: B:G.175, B:G.338 Water bridges: B:R.68, B:R.103 Salt bridges: B:R.68, B:R.103

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

FAD.2: 31 residues within 4Å: Chain A: G.15, G.17, I.18, S.19, V.39, E.40, S.41, G.47, W.48, I.49, L.62, G.63, P.64, Q.65, G.66, Q.261, P.262, V.263, A.291, I.292, V.296, V.322, C.424, I.425, G.454, A.455, V.460, A.461, V.462, C.465 Ligands: ACJ.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.48, A:V.322, A:I.425 Hydrogen bonds: A:G.15, A:G.16, A:G.17, A:S.19, A:S.19, A:S.19, A:S.41, A:S.41, A:G.47, A:W.48, A:Q.65, A:G.66, A:G.66, A:V.263, A:V.263, A:A.455, A:V.462 Water bridges: A:I.18, A:I.18, A:G.20, A:G.47 FAD.6: 31 residues within 4Å: Chain B: G.15, G.17, I.18, S.19, V.39, E.40, S.41, G.47, W.48, I.49, L.62, G.63, P.64, Q.65, G.66, Q.261, P.262, V.263, A.291, I.292, V.296, V.322, C.424, I.425, G.454, A.455, V.460, A.461, V.462, C.465 Ligands: ACJ.5 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:W.48, B:V.322, B:I.425 Hydrogen bonds: B:G.15, B:G.16, B:G.17, B:S.19, B:S.19, B:S.19, B:S.41, B:S.41, B:G.47, B:W.48, B:Q.65, B:G.66, B:G.66, B:V.263, B:V.263, B:A.455, B:V.462 Water bridges: B:I.18, B:I.18, B:G.20, B:G.47

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.431, Q.434, K.435, S.438 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.434, A:S.438, A:S.438 GOL.4: 5 residues within 4Å: Chain A: R.187, W.433, E.437, 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.434, B:S.438, B:S.438 GOL.8: 5 residues within 4Å: Chain B: R.187, W.433, E.437, 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

Related Entries With Identical Sequence