SMTL ID : 6ebs.1

Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant H174A in complex with orotate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: A.53, A.54, G.55, V.56, K.78, S.79, Y.93, N.102, M.104, N.162, K.199, I.228, N.229, S.230, G.256, G.257, V.260, C.283, G.284, G.285, G.306, T.307 Ligands: ORO.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.56, A:Y.93, A:Y.93 Hydrogen bonds: A:A.54, A:S.79, A:S.79, A:S.79, A:N.162, A:K.199, A:K.199, A:N.229, A:G.257, A:G.285, A:G.306, A:T.307, A:T.307 Water bridges: A:G.284, A:G.284, A:V.286, A:V.286 FMN.9: 23 residues within 4Å: Chain B: A.53, A.54, G.55, V.56, K.78, S.79, Y.93, N.102, M.104, N.162, K.199, I.228, N.229, S.230, G.256, G.257, V.260, C.283, G.284, G.285, G.306, T.307 Ligands: ORO.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.56, B:Y.93, B:Y.93 Hydrogen bonds: B:A.54, B:S.79, B:S.79, B:S.79, B:K.199, B:K.199, B:N.229, B:G.257, B:G.285, B:G.306, B:T.307 Water bridges: B:G.284, B:G.284, B:V.286, B:V.286

2 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 residues within 4Å: Chain A: K.78, N.102, S.103, M.104, G.105, L.106, N.162, C.165, P.166, N.167, N.229, S.230 Ligands: FMN.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.102, A:N.102, A:N.102, A:M.104, A:G.105, A:L.106, A:N.162, A:N.167, A:N.229, A:N.229, A:S.230 Salt bridges: A:K.78 ORO.10: 12 residues within 4Å: Chain B: K.78, N.102, M.104, G.105, L.106, N.162, C.165, P.166, N.167, N.229, S.230 Ligands: FMN.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.102, B:N.102, B:M.104, B:G.105, B:L.106, B:N.162, B:N.167, B:N.229, B:N.229, B:S.230 Salt bridges: B:K.78

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.236, I.237 Chain B: L.261, L.265, L.294 Ligands: SO4.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.237 Water bridges: A:Y.259, B:D.291 GOL.4: 9 residues within 4Å: Chain A: D.205, F.206, A.207 Chain B: P.166, K.171, P.172, Q.173, N.233, K.249 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.205, A:F.206, A:A.207, B:P.166, B:Q.173, B:N.233, B:K.249 GOL.5: 9 residues within 4Å: Chain A: P.166, K.171, P.172, Q.173, N.233, K.249 Chain B: D.205, F.206, A.207 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.173, A:N.233, A:N.233, A:K.249, B:F.206, B:A.207 Water bridges: A:C.165, A:V.168 GOL.11: 7 residues within 4Å: Chain A: L.261, L.265, L.294 Chain B: P.97, V.236, I.237 Ligands: SO4.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.237, B:I.237

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

SO4.6: 2 residues within 4Å: Chain A: H.194, S.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.195 Salt bridges: A:H.194 SO4.7: 2 residues within 4Å: Chain A: R.273, T.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.345 Water bridges: A:R.273, A:R.273, A:T.345 Salt bridges: A:R.273 SO4.8: 5 residues within 4Å: Chain A: L.96, P.97, V.236, D.238 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.238 Water bridges: A:A.239 SO4.12: 3 residues within 4Å: Chain B: N.43, H.194, S.195 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.43, B:S.195, B:S.195 Salt bridges: B:H.194 SO4.13: 3 residues within 4Å: Chain A: Q.250 Chain B: R.273, T.345 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.345, B:T.345 Water bridges: B:R.273, B:R.273 Salt bridges: B:R.273 SO4.14: 5 residues within 4Å: Chain B: L.96, P.97, V.236, D.238 Ligands: GOL.11 No protein-ligand interaction detected (PLIP)

1 x NI: NICKEL (II) ION(Non-covalent)

NI.15: 2 residues within 4Å: Chain B: Y.176, F.204 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reis, R.A.G. et al., Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant H174A in complex with orotate. To Be Published

Release Date

2019-08-21

Peptides

Dihydroorotate dehydrogenase (fumarate): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase (fumarate)