SMTL ID : 2prl.1

The structures of apo- and inhibitor bound human dihydroorotate dehydrogenase reveal conformational flexibility within the inhibitor binding site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.216, V.218, H.219 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.216, A:H.219

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

ACT.2: 4 residues within 4Å: Chain A: D.282, T.285, Q.286, R.289 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.282, A:Q.286 Salt bridges: A:R.289 ACT.3: 7 residues within 4Å: Chain A: E.24, H.27, R.28, K.71, H.72, Y.118, N.121 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.28, A:Y.118 Hydrogen bonds: A:N.121 Salt bridges: A:H.27, A:H.72

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 25 residues within 4Å: Chain A: A.66, A.67, G.68, K.71, G.90, S.91, N.116, Y.118, N.152, N.183, K.226, T.254, N.255, T.256, S.276, G.277, L.280, V.304, G.305, G.306, L.326, Y.327, T.328 Ligands: ORO.5, R2C.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.116, A:Y.118, A:Y.118, A:Y.327, A:Y.327 Hydrogen bonds: A:A.67, A:K.71, A:S.91, A:S.91, A:N.152, A:K.226, A:K.226, A:N.255, A:S.276, A:G.277, A:G.306, A:Y.327, A:T.328 Water bridges: A:A.67, A:G.305, A:G.305

1 x ORO: OROTIC ACID(Non-covalent)

ORO.5: 13 residues within 4Å: Chain A: K.71, N.116, R.117, Y.118, G.119, F.120, N.183, S.186, P.187, N.188, N.255, T.256 Ligands: FMN.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.120 Hydrogen bonds: A:N.116, A:N.116, A:N.116, A:G.119, A:F.120, A:N.183, A:N.188, A:N.255, A:N.255, A:T.256 Water bridges: A:S.186, A:S.186 Salt bridges: A:K.71

1 x R2C: 5-METHOXY-2-[(4-PHENOXYPHENYL)AMINO]BENZOIC ACID(Non-covalent)

R2C.6: 19 residues within 4Å: Chain A: Y.9, L.13, M.14, L.17, Q.18, P.23, A.26, H.27, A.30, F.33, L.38, V.105, R.107, Y.327, L.330, T.331, P.335 Ligands: FMN.4, DDQ.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.9, A:L.13, A:L.17, A:A.26, A:H.27, A:A.30, A:A.30, A:F.33, A:T.331, A:T.331 Hydrogen bonds: A:Q.18, A:Y.327, A:T.331 Salt bridges: A:R.107

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

DDQ.7: 7 residues within 4Å: Chain A: A.2, Y.9, L.17, F.33, L.38, L.39 Ligands: R2C.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.2, A:L.17, A:F.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walse, B. et al., The structures of human dihydroorotate dehydrogenase with and without inhibitor reveal conformational flexibility in the inhibitor and substrate binding sites. Biochemistry (2008)

Release Date

2008-05-20

Peptides

Dihydroorotate dehydrogenase, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase, mitochondrial

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