SMTL ID : 4js3.1

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 057

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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 20 PLIP interactions: 20 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

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 12 residues within 4Å: Chain A: K.94, N.139, R.140, Y.141, G.142, F.143, N.206, S.209, N.211, N.278, T.279 Ligands: FMN.1 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

1 x JS3: 2-chloro-4-methyl-N-(naphthalen-2-yl)-1,3-thiazole-5-carboxamide(Non-covalent)

JS3.3: 12 residues within 4Å: Chain A: Y.32, L.36, M.37, A.53, F.56, T.57, L.61, L.62, M.105, L.353, P.358 Ligands: ACY.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.32, A:A.53, A:F.56, A:L.353, A:P.358 Hydrogen bonds: A:L.61

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

SO4.4: 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 SO4.5: 6 residues within 4Å: Chain A: R.51, H.95, R.125, R.127, N.144, H.146 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.47, A:R.125, A:R.127, A:N.144 Water bridges: A:R.51, A:R.51, A:R.51, A:S.145 Salt bridges: A:R.51, A:H.95 SO4.6: 1 residues within 4Å: Chain A: R.154 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.154 SO4.7: 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:S.256 SO4.8: 2 residues within 4Å: Chain A: R.240, R.243 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.243, A:R.243 Salt bridges: A:R.240, A:R.243 SO4.9: 3 residues within 4Å: Chain A: A.213, G.214, R.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.214 Water bridges: A:T.212, A:R.216 Salt bridges: A:R.216 SO4.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

5 x ACY: ACETIC ACID(Non-functional Binders)

ACY.11: 4 residues within 4Å: Chain A: D.305, T.308, Q.309, R.312 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.305, A:Q.309 Water bridges: A:Q.309 Salt bridges: A:R.312 ACY.12: 6 residues within 4Å: Chain A: Q.162, A.163, T.166, L.199, A.200, D.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.201 Water bridges: A:E.167 ACY.13: 6 residues within 4Å: Chain A: H.50, A.53, F.92, Y.350, T.354 Ligands: JS3.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.53 Hydrogen bonds: A:Y.350 Salt bridges: A:H.50 ACY.14: 3 residues within 4Å: Chain A: K.221, D.261, S.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.261, A:S.264, A:S.264 Water bridges: A:S.264 Salt bridges: A:K.221 ACY.15: 2 residues within 4Å: Chain A: K.221, R.225 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.221 Salt bridges: A:K.221, A:R.225

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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