SMTL ID : 6ywt.1

Human OMPD-domain of UMPS (K314AcK) in complex with 6-hydroxy-UMP at 1.05 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

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

BMP.1: 18 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, Q.210, Y.212, V.229, G.230, R.231 Chain B: D.97, I.98, T.101 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.181, A:P.197 Hydrogen bonds: A:S.37, A:D.39, A:D.39, A:K.61, A:D.92, A:S.152, A:S.152, A:S.152, A:Q.210, A:Y.212, A:Y.212, A:Y.212, A:G.230, A:R.231, B:T.101, B:T.101 Water bridges: A:G.198, A:G.198, A:Q.200 Salt bridges: A:R.231 BMP.4: 18 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, Q.210, Y.212, V.229, G.230, R.231 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.181, B:P.197 Hydrogen bonds: B:S.37, B:D.39, B:K.61, B:D.92, B:S.152, B:S.152, B:S.152, B:Q.210, B:Y.212, B:Y.212, B:G.230, B:R.231, A:T.101 Water bridges: B:G.198, B:G.198, B:Q.200 Salt bridges: B:R.231

4 x PRO: PROLINE(Non-covalent)

PRO.2: 2 residues within 4Å: Chain A: L.201, A.203 3 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: P.2, P.2 Water bridges: A:S.214 PRO.3: 6 residues within 4Å: Chain A: Q.200, E.202, A.203, G.204, G.205, Y.212 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.212 Hydrogen bonds: A:A.203, A:G.205, P.3 PRO.5: 2 residues within 4Å: Chain B: L.201, A.203 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Ligand interactions Water bridges: B:S.214 Hydrogen bonds: P.5, P.5 PRO.6: 6 residues within 4Å: Chain B: Q.200, E.202, A.203, G.204, G.205, Y.212 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.212 Hydrogen bonds: B:A.203, B:G.205, P.6

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

2022-02-23

Peptides

Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Uridine 5'-monophosphate synthase

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