SMTL ID : 3w7r.1

Structure of Human dihydroorotate dehydrogenase in complex with mii-4-097

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: R.292, S.293 Ligand excluded by PLIP

6 x DDQ: DECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DDQ.2: 4 residues within 4Å: Chain A: E.34, H.35, T.39 Ligands: DDQ.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.35, A:T.39 DDQ.3: 5 residues within 4Å: Chain A: P.38, T.39, G.42 Ligands: DDQ.2, DDQ.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.39 DDQ.4: 4 residues within 4Å: Chain A: Q.41, G.42, L.43 Ligands: DDQ.3 No protein-ligand interaction detected (PLIP) DDQ.5: 1 residues within 4Å: Chain A: F.56 No protein-ligand interaction detected (PLIP) DDQ.6: 5 residues within 4Å: Chain A: G.27, R.30, F.31, E.34, H.35 No protein-ligand interaction detected (PLIP) DDQ.7: 8 residues within 4Å: Chain A: Y.32, L.36, L.52, A.53, F.56, L.61, L.62 Ligands: W7A.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.36, A:L.52, A:F.56, A:F.56

1 x W7A: 2,6-dioxo-5-[2-(4-phenylphenyl)ethyl]-1,2,3,6- tetrahydropyrimidine-4-carboxylic acid(Non-covalent)

W7A.8: 20 residues within 4Å: Chain A: Y.32, M.37, L.40, P.46, A.49, H.50, A.53, F.56, T.57, L.61, L.62, F.92, V.128, R.130, Y.350, L.353, T.354, P.358 Ligands: DDQ.7, FMN.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.32, A:L.40, A:A.53, A:F.56, A:L.62, A:L.353, A:P.358 Hydrogen bonds: A:Y.350, A:Y.350 Salt bridges: A:R.130

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.9: 25 residues within 4Å: Chain A: A.89, A.90, G.91, K.94, G.113, S.114, N.139, Y.141, N.175, N.206, K.249, T.277, N.278, T.279, S.299, G.300, L.303, V.327, G.328, G.329, L.349, Y.350, T.351 Ligands: W7A.8, ORO.32 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:N.139, A:Y.141, A:Y.350, A:Y.350 Hydrogen bonds: A:A.90, A:K.94, A:S.114, A:S.114, A:N.175, A:K.249, A:N.278, A:S.299, A:G.300, A:G.329, A:Y.350, A:T.351 Water bridges: A:A.90, A:G.328, A:V.330

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: D.305, T.308, Q.309, R.312, E.338 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: Y.315, A.316, Q.319, H.388 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: R.216, S.217, Q.219, G.220, D.258 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: R.51, H.95, N.144, H.146 Ligands: GOL.16 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: V.54, R.55, S.58, E.97 Ligands: ACT.39 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: A.213, G.214, R.216 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: P.119, Q.120, E.121, S.145, H.146 Ligands: GOL.13 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: E.133, Q.288, G.289, A.290 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain A: R.130, P.132, L.291 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: R.235, R.243, P.244, A.245 Ligands: GOL.20 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain A: H.80, D.201, R.240, V.241, R.243 Ligands: GOL.19, ACT.38 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: H.80, K.81, T.166, E.167, P.171 Ligands: ACT.42 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain A: D.45, P.46, P.126, V.128, F.129 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain A: M.24, T.26, G.27, R.66 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain A: P.117, K.118, E.191, V.195 Ligands: ACT.37 Ligand excluded by PLIP GOL.25: 9 residues within 4Å: Chain A: L.62, P.63, R.64, A.65, M.105, P.358, P.359, V.361, G.362 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain A: E.74, V.75, R.76, T.381 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain A: V.266, K.267, G.270, I.271, V.322 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Chain A: K.221, R.225 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain A: T.255, Q.257, D.258 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain A: M.24, R.366, E.367, A.370 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain A: Q.135, K.301, S.331, S.332, W.356, K.363 Ligand excluded by PLIP

1 x ORO: OROTIC ACID(Non-covalent)

ORO.32: 13 residues within 4Å: Chain A: K.94, N.139, R.140, Y.141, G.142, F.143, N.206, S.209, P.210, N.211, N.278, T.279 Ligands: FMN.9 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.143 Hydrogen bonds: A:N.139, A:N.139, A:Y.141, A:G.142, A:F.143, A:N.206, A:N.211, A:N.278, A:N.278, A:T.279 Water bridges: A:S.209, A:S.209 Salt bridges: A:K.94

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

SO4.33: 3 residues within 4Å: Chain A: R.239, V.241, H.242 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.239, A:H.242 SO4.34: 2 residues within 4Å: Chain A: R.154 Ligands: ACT.39 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.154, A:R.154, A:R.154 Salt bridges: A:R.154 SO4.35: 6 residues within 4Å: Chain A: R.76, V.77, L.78, G.79, H.80 Ligands: ACT.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.79, A:H.80 Water bridges: A:L.78, A:L.78 SO4.36: 2 residues within 4Å: Chain A: R.240, R.243 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.240, A:R.243 Salt bridges: A:R.243

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.37: 4 residues within 4Å: Chain A: K.118, P.119, S.149 Ligands: GOL.24 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.118 ACT.38: 7 residues within 4Å: Chain A: Q.162, A.163, T.166, L.199, A.200, D.201 Ligands: GOL.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.166 Hydrogen bonds: A:A.200 ACT.39: 4 residues within 4Å: Chain A: E.97, R.154 Ligands: GOL.14, SO4.34 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.97 Salt bridges: A:R.154 ACT.40: 6 residues within 4Å: Chain A: T.57, S.58, L.59, G.60, G.101, K.104 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.101, A:K.104 Salt bridges: A:K.104 ACT.41: 4 residues within 4Å: Chain A: Q.159, Q.160, A.163, H.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.159 Salt bridges: A:H.242 ACT.42: 6 residues within 4Å: Chain A: R.76, V.77, G.79, H.80 Ligands: GOL.21, SO4.35 No protein-ligand interaction detected (PLIP) ACT.43: 3 residues within 4Å: Chain A: A.222, E.223, R.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaoka, D.K. et al., Structure of Human dihydroorotate dehydrogenase in complex with mii-4-097. To be Published

Release Date

2014-03-12

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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