SMTL ID : 4jtu.1 (1 other biounit)

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with brequinar analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 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: ORO.2, JTU.7 24 PLIP interactions: 24 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:K.249, A:N.278, A:S.299, A:S.299, A:G.300, A:G.329, A:Y.350, A:T.351, A:T.351 Water bridges: A:A.90, A:G.328, A:V.330, A:V.330, A:V.330 FMN.8: 25 residues within 4Å: Chain B: 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: ORO.9, JTU.14 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:N.139, B:Y.141, B:Y.350, B:Y.350 Hydrogen bonds: B:A.90, B:K.94, B:S.114, B:S.114, B:N.175, B:K.249, B:K.249, B:N.278, B:S.299, B:S.299, B:G.300, B:G.329, B:Y.350, B:T.351 Water bridges: B:A.90, B:G.328, B:V.330, B:V.330, B:V.330

2 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 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.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.143 Hydrogen bonds: A:N.139, A:N.139, A:N.139, A:G.142, A:F.143, A:N.206, A:N.211, A:N.278, A:N.278 Water bridges: A:S.209, A:S.209 Salt bridges: A:K.94 ORO.9: 13 residues within 4Å: Chain B: 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.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.143 Hydrogen bonds: B:N.139, B:N.139, B:N.139, B:G.142, B:F.143, B:N.206, B:N.211, B:N.278, B:N.278, B:T.279 Water bridges: B:S.209, B:S.209 Salt bridges: B:K.94

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

SO4.3: 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 SO4.4: 1 residues within 4Å: Chain A: R.154 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.154 SO4.5: 7 residues within 4Å: Chain A: D.305, T.308, Q.309, R.312 Chain B: K.301, P.302, R.304 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.301, A:R.312 Hydrogen bonds: A:Q.309 Water bridges: A:D.305 SO4.10: 3 residues within 4Å: Chain B: R.239, V.241, H.242 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.239, B:H.242 SO4.11: 1 residues within 4Å: Chain B: R.154 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.154 SO4.12: 7 residues within 4Å: Chain A: K.301, P.302, R.304 Chain B: D.305, T.308, Q.309, R.312 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.301, B:R.312 Hydrogen bonds: B:Q.309

2 x DET: UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DET.6: 7 residues within 4Å: Chain A: R.51, H.95, P.119, Q.120, E.121, S.145, H.146 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.119, A:E.121 Hydrogen bonds: A:R.51, A:R.51 DET.13: 7 residues within 4Å: Chain B: R.51, H.95, P.119, Q.120, E.121, S.145, H.146 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.119, B:E.121 Hydrogen bonds: B:R.51, B:R.51

2 x JTU: 6-bromo-2-{4-[(2R)-butan-2-yl]phenyl}-3-methylquinoline-4-carboxylic acid(Non-covalent)

JTU.7: 15 residues within 4Å: Chain A: M.37, Q.41, P.46, A.49, H.50, A.53, T.57, L.62, V.128, R.130, Y.350, L.353, T.354, P.358 Ligands: FMN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.49, A:H.50, A:A.53, A:L.62, A:Y.350, A:T.354, A:T.354, A:P.358 Hydrogen bonds: A:Q.41 Water bridges: A:T.354 Salt bridges: A:R.130 JTU.14: 15 residues within 4Å: Chain B: M.37, Q.41, P.46, A.49, H.50, A.53, T.57, L.62, V.128, R.130, Y.350, L.353, T.354, P.358 Ligands: FMN.8 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.49, B:H.50, B:A.53, B:L.62, B:Y.350, B:T.354, B:T.354, B:P.358 Hydrogen bonds: B:Q.41 Water bridges: B:T.354 Salt bridges: B:R.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, L. et al., Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 057. To be Published

Release Date

2014-03-26

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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