SMTL ID : 8dhk.1

Crystal structure of human Sulfide Quinone Oxidoreductase K207E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 39 residues within 4Å: Chain A: G.10, G.11, G.12, S.13, G.14, G.15, V.34, E.35, P.36, S.37, Q.43, P.44, W.46, T.47, A.76, R.77, V.78, A.104, L.105, G.106, N.129, Y.130, K.160, C.161, A.164, P.261, V.263, G.295, D.296, C.297, K.304, T.305, A.306, A.307, V.309, S.338, C.339, P.340, K.378 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:Y.130, A:Y.130, A:A.164 Hydrogen bonds: A:G.12, A:S.13, A:S.13, A:G.14, A:E.35, A:E.35, A:Q.43, A:R.77, A:V.78, A:V.78, A:G.106, A:D.296, A:D.296, A:A.306, A:A.307, A:S.338, A:K.378 Water bridges: A:S.13, A:S.37, A:H.40, A:Q.43, A:I.107, A:K.160, A:K.160, A:C.297 Salt bridges: A:K.160 FAD.9: 39 residues within 4Å: Chain B: G.10, G.11, G.12, S.13, G.14, G.15, V.34, E.35, P.36, S.37, Q.43, P.44, W.46, T.47, A.76, R.77, V.78, A.104, L.105, G.106, N.129, Y.130, K.160, C.161, A.164, P.261, V.263, G.295, D.296, C.297, K.304, T.305, A.306, A.307, V.309, S.338, C.339, P.340, K.378 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:Y.130, B:Y.130 Hydrogen bonds: B:S.13, B:G.14, B:E.35, B:E.35, B:Q.43, B:R.77, B:R.77, B:V.78, B:V.78, B:G.106, B:D.296, B:D.296, B:A.306, B:A.307, B:S.338, B:K.378 Water bridges: B:G.12, B:S.13, B:G.15, B:S.37, B:H.40, B:Q.43, B:I.107, B:K.160, B:C.297, B:T.305 Salt bridges: B:K.160 pi-Cation interactions: B:R.77

11 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 10 residues within 4Å: Chain A: Y.42, A.306, A.307, A.310, M.382, L.385, Y.386, M.389, M.390, W.395 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.42 PEG.4: 9 residues within 4Å: Chain A: F.154, A.162, L.193, F.197, G.198, V.199, S.303, F.353, A.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.198 PEG.5: 8 residues within 4Å: Chain A: K.201, P.359, E.361, F.363, P.364, F.365, D.366, Q.367 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.201, A:E.361, A:E.361 PEG.7: 3 residues within 4Å: Chain A: D.380, L.381, F.384 No protein-ligand interaction detected (PLIP) PEG.8: 7 residues within 4Å: Chain A: A.51, G.52, A.53, W.139, Y.175, K.178, Y.345 No protein-ligand interaction detected (PLIP) PEG.10: 9 residues within 4Å: Chain B: Y.42, A.306, A.307, A.310, M.382, L.385, Y.386, M.390, W.395 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.42 PEG.11: 7 residues within 4Å: Chain B: A.51, G.52, A.53, W.139, Y.175, K.178, Y.345 No protein-ligand interaction detected (PLIP) PEG.12: 7 residues within 4Å: Chain B: A.162, F.197, G.198, V.199, S.303, F.353, A.357 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.198, B:S.303 PEG.13: 7 residues within 4Å: Chain B: R.39, F.41, L.56, S.57, G.60, R.61, P.62 No protein-ligand interaction detected (PLIP) PEG.14: 6 residues within 4Å: Chain B: P.83, D.84, N.86, Y.288, P.289, N.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.86, B:N.290 PEG.19: 4 residues within 4Å: Chain B: F.365, D.366, K.369, R.371 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.366, B:R.371, B:R.371

2 x MHA: (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID(Non-covalent)

MHA.3: 7 residues within 4Å: Chain A: Q.207, I.210, Q.211, L.215, T.216, V.217, Y.219 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.207, A:Q.207, A:Q.211, A:V.217, A:V.217, A:Y.219 MHA.15: 3 residues within 4Å: Chain B: F.384, N.388, R.392 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.392

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 3 residues within 4Å: Chain A: S.37, E.38, R.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.38, A:R.39 SO4.16: 3 residues within 4Å: Chain B: R.371, L.372, S.373 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.372, B:S.373, B:S.373, B:S.373 Salt bridges: B:R.371 SO4.17: 4 residues within 4Å: Chain B: S.37, E.38, R.39, F.41 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.37, B:E.38, B:R.39 Salt bridges: B:R.39 SO4.18: 3 residues within 4Å: Chain B: K.54, Q.55, S.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.55, B:S.58 Salt bridges: B:K.54

Links

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Citation

Bonanata, J. et al., Sulfide oxidation in human sulfide quinone oxidoreductase is enthalpically driven: Contributions of the Lys-207 general base. To Be Published

Release Date

2023-07-19

Peptides

Sulfide:quinone oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sulfide:quinone oxidoreductase