SMTL ID : 7otu.1

Human OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.95 Angstroms resolution, crystal 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.95 Å

Oligo State

homo-dimer

Ligands

2 x BMP: 6-HYDROXYURIDINE-5'-PHOSPHATE(Non-covalent)

BMP.1: 21 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, D.92, K.94, M.151, S.152, I.181, P.197, G.198, Q.210, Y.212, I.228, V.229, G.230, R.231, G.232 Chain B: D.97, I.98, T.101 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.197 Hydrogen bonds: A:D.39, A:D.39, A:K.61, A:H.63, A:D.92, A:D.92, A:K.94, A:S.152, A:S.152, A:Q.210, A:Y.212, A:Y.212, A:Y.212, A:G.230, A:R.231 Water bridges: A:G.198, A:G.198, A:Q.200, A:R.231 Salt bridges: A:R.231 BMP.4: 21 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, D.39, K.61, H.63, D.92, K.94, M.151, S.152, I.181, P.197, G.198, Q.210, Y.212, I.228, V.229, G.230, R.231, G.232 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.197 Hydrogen bonds: B:D.39, B:K.61, B:H.63, B:D.92, B:D.92, B:K.94, B:S.152, B:S.152, B:Q.210, B:Y.212, B:Y.212, B:Y.212, B:G.230, B:R.231 Water bridges: B:G.198, B:G.198, B:Q.200, B:R.231 Salt bridges: B:R.231

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: G.160, R.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.164, A:R.164 Water bridges: A:G.160, A:D.161 GOL.3: 9 residues within 4Å: Chain A: K.22, I.79, A.82, K.83, E.86, F.87, L.88, I.89, D.118 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.22, A:F.87, A:F.87, A:D.118, A:D.118 Water bridges: A:I.89 GOL.5: 2 residues within 4Å: Chain B: G.160, R.164 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.164, B:R.164 Water bridges: B:G.160, B:D.161 GOL.6: 9 residues within 4Å: Chain B: K.22, I.79, A.82, K.83, E.86, F.87, L.88, I.89, D.118 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.22, B:F.87, B:F.87, B:D.118, B:D.118 Water bridges: B:I.89, B:D.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rindfleisch, S. et al., Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis. Nat Catal (2022)

Release Date

2022-04-20

Peptides

Isoform 2 of Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Isoform 2 of Uridine 5'-monophosphate synthase

Related Entries With Identical Sequence