SMTL ID : 7ouz.1

Human OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.9 Angstroms resolution, crystal 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.90 Å

Oligo State

homo-dimer

Ligands

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

BMP.1: 21 residues within 4Å: Chain A: S.35, D.37, K.59, H.61, D.90, K.92, M.149, S.150, I.179, P.195, G.196, Q.208, Y.210, I.226, V.227, G.228, R.229, G.230 Chain B: D.95, I.96, T.99 22 PLIP interactions: 2 interactions with chain B, 20 interactions with chain A Hydrogen bonds: B:T.99, A:D.37, A:K.59, A:H.61, A:D.90, A:D.90, A:K.92, A:S.150, A:S.150, A:Q.208, A:Y.210, A:Y.210, A:Y.210, A:G.228, A:R.229 Water bridges: B:N.98, A:G.196, A:G.196, A:Q.198, A:R.229 Hydrophobic interactions: A:P.195 Salt bridges: A:R.229 BMP.4: 21 residues within 4Å: Chain A: D.95, I.96, T.99 Chain B: S.35, D.37, K.59, H.61, D.90, K.92, M.149, S.150, I.179, P.195, G.196, Q.208, Y.210, I.226, V.227, G.228, R.229, G.230 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.195 Hydrogen bonds: B:K.59, B:H.61, B:D.90, B:D.90, B:K.92, B:S.150, B:S.150, B:Q.208, B:Y.210, B:Y.210, B:Y.210, B:G.228, B:R.229, A:T.99 Water bridges: B:G.196, B:G.196, B:Q.198, B:R.229, A:N.98 Salt bridges: B:R.229

2 x PRO: PROLINE(Non-covalent)

PRO.2: 4 residues within 4Å: Chain A: L.199, E.200, A.201, S.212 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Water bridges: A:S.212 Hydrogen bonds: P.2, P.2 PRO.5: 4 residues within 4Å: Chain B: L.199, E.200, A.201, S.212 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Ligand interactions Water bridges: B:S.212 Hydrogen bonds: P.5, P.5

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: R.42 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.42, A:R.42 GOL.6: 1 residues within 4Å: Chain B: R.42 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.42, B:R.42

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

Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Uridine 5'-monophosphate synthase