SMTL ID : 3nks.2 (1 other biounit)

Structure of human protoporphyrinogen IX oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.97, R.168, G.169, V.170, F.171, A.172, F.331, G.332, H.333, L.334, L.344, G.345, I.346, V.347, M.368, I.419 Ligands: FAD.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.334, A:L.334, A:V.347 Water bridges: A:R.97 Salt bridges: A:R.97 ACJ.5: 17 residues within 4Å: Chain B: R.97, R.168, G.169, V.170, F.171, A.172, F.331, G.332, H.333, L.334, L.344, G.345, I.346, V.347, M.368, I.419 Ligands: FAD.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.334, B:L.334, B:V.347 Water bridges: B:R.97 Salt bridges: B:R.97

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

FAD.2: 28 residues within 4Å: Chain A: G.9, G.11, I.12, S.13, V.33, E.34, S.35, G.41, W.42, L.56, G.57, P.58, R.59, G.60, P.256, V.257, A.285, I.286, V.290, V.316, C.418, G.448, A.449, V.454, A.455, V.456, C.459 Ligands: ACJ.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.316 Hydrogen bonds: A:G.9, A:S.13, A:S.13, A:S.13, A:S.35, A:S.35, A:G.41, A:W.42, A:R.59, A:G.60, A:V.257, A:V.257, A:A.449, A:V.456 Water bridges: A:G.11, A:I.12, A:I.12, A:G.14, A:S.36, A:N.457 FAD.6: 28 residues within 4Å: Chain B: G.9, G.11, I.12, S.13, V.33, E.34, S.35, G.41, W.42, L.56, G.57, P.58, R.59, G.60, P.256, V.257, A.285, I.286, V.290, V.316, C.418, G.448, A.449, V.454, A.455, V.456, C.459 Ligands: ACJ.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.316 Hydrogen bonds: B:G.9, B:S.13, B:S.13, B:S.13, B:S.35, B:S.35, B:G.41, B:W.42, B:R.59, B:G.60, B:V.257, B:V.257, B:A.449, B:V.456 Water bridges: B:G.11, B:I.12, B:I.12, B:G.14, B:S.36, B:N.457

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.425, Q.428, K.429, S.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.428, A:S.432 GOL.4: 4 residues within 4Å: Chain A: W.427, E.431, R.434, E.452 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.434, A:E.452 Water bridges: A:E.452, A:E.452 GOL.7: 4 residues within 4Å: Chain B: G.425, Q.428, K.429, S.432 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.428, B:S.432 GOL.8: 4 residues within 4Å: Chain B: W.427, E.431, R.434, E.452 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.434, B:E.452 Water bridges: B:E.452, B:E.452

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, X. et al., Structural insight into human variegate porphyria disease. Faseb J. (2011)

Release Date

2011-04-20

Peptides

Protoporphyrinogen oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protoporphyrinogen oxidase

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