SMTL ID : 4jgd.1

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A016

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 24 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 22 PLIP interactions: 22 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:G.300, A:G.329, A:Y.350, A:T.351 Water bridges: A:A.90, A:G.328, A:V.330, A:V.330, A:V.330

1 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: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

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

DET.3: 12 residues within 4Å: Chain A: E.47, H.50, R.51, K.94, H.95, P.119, Q.120, E.121, Y.141, N.144, S.145, H.146 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.119, A:N.144 Hydrogen bonds: A:H.50 pi-Cation interactions: A:H.50

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

SO4.4: 3 residues within 4Å: Chain A: R.239, V.241, H.242 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.241 Salt bridges: A:R.239, A:H.242 SO4.5: 6 residues within 4Å: Chain A: G.27, A.65, R.66, F.67, G.362, R.366 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.27, A:G.27, A:R.66, A:F.67 Water bridges: A:G.362, A:R.366 Salt bridges: A:R.366 SO4.6: 3 residues within 4Å: Chain A: K.301, P.302, R.304 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.304 SO4.7: 1 residues within 4Å: Chain A: R.154 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.154 SO4.8: 4 residues within 4Å: Chain A: R.239, R.240, R.243 Ligands: SO4.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.240, A:R.243 Salt bridges: A:R.239 SO4.9: 3 residues within 4Å: Chain A: R.240, R.243 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.243 SO4.10: 3 residues within 4Å: Chain A: T.255, Q.257, D.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.255, A:T.255 Water bridges: A:Q.257 SO4.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.12: 3 residues within 4Å: Chain A: A.213, G.214, R.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.214, A:L.215 Water bridges: A:T.212, A:R.216 Salt bridges: A:R.216

1 x 4JG: 1-[4-methyl-2-(naphthalen-2-ylamino)-1,3-thiazol-5-yl]ethanone(Non-covalent)

4JG.13: 14 residues within 4Å: Chain A: M.37, L.40, P.46, A.49, H.50, A.53, T.57, L.62, F.92, M.105, Y.350, L.353, T.354, P.358 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.40, A:P.46, A:H.50, A:A.53, A:L.62, A:L.353, A:P.358 Hydrogen bonds: A:Y.350, A:T.354 Water bridges: A:Q.41, A:Q.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, L. et al., Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A016. TO BE PUBLISHED

Release Date

2014-03-05

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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