SMTL ID : 6zx1.1

OMPD-domain of human UMPS in complex with 6-Aza-UMP at 1.0 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-dimer

Ligands

2 x UP6: 6-AZA URIDINE 5'-MONOPHOSPHATE(Non-covalent)

UP6.1: 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 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.37, A:D.39, A:K.61, A:K.94, 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:K.94, A:G.198, A:V.199, A:Q.200 Salt bridges: A:R.231 UP6.5: 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 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.37, B:K.61, B:K.94, B:S.152, B:Q.210, B:G.230, B:R.231, A:D.97, A:T.101 Water bridges: B:K.94, B:G.198, B:V.199, B:Q.200 Salt bridges: B:R.231

4 x PRO: PROLINE(Non-covalent)

PRO.2: 3 residues within 4Å: Chain A: G.8, A.9, E.12 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: P.2, P.2 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.6: 3 residues within 4Å: Chain B: G.8, A.9, E.12 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: P.6, P.6 PRO.7: 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.7

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

SO4.4: 2 residues within 4Å: Chain A: N.213, R.222 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.213 Water bridges: A:S.152, A:Q.211, A:Q.211, A:R.222 Salt bridges: A:R.222 SO4.8: 2 residues within 4Å: Chain B: N.213, R.222 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.213 Water bridges: B:S.152, B:Q.211, B:Q.211, B:R.222 Salt bridges: B:R.222

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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