SMTL ID : 6zwy.1

OMPD-domain of human UMPS in complex with UMP at 1.0 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-dimer

Ligands

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 17 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, D.92, K.94, M.151, S.152, P.197, Q.210, Y.212, V.229, G.230, R.231 Chain B: D.97, I.98, T.101 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.197 Hydrogen bonds: A:S.37, A:D.39, A:K.61, A:S.152, A:S.152, A:S.152, A:Q.210, A:Y.212, A:G.230, A:R.231, B:D.97, B:T.101, B:T.101 Water bridges: A:G.198, A:V.199, A:Q.200 Salt bridges: A:R.231 U5P.5: 17 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, P.197, Q.210, Y.212, V.229, G.230, R.231 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.197 Hydrogen bonds: B:S.37, B:K.61, B:S.152, B:S.152, B:S.152, B:Q.210, B:G.230, B:R.231, A:D.97, A:T.101 Water bridges: B:G.198, B:V.199, B:Q.200 Salt bridges: B:R.231

2 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.6: 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.6, P.6

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: R.44 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.44 GOL.4: 6 residues within 4Å: Chain A: Q.200, L.201, E.202, G.232, A.236, Y.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.201, A:E.202 Water bridges: A:Y.246 GOL.7: 1 residues within 4Å: Chain B: R.44 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.44 GOL.8: 6 residues within 4Å: Chain B: Q.200, L.201, E.202, G.232, A.236, Y.246 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.201, B:E.202, B:Y.246

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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