SMTL ID : 7oqm.1

Human OMPD-domain of UMPS in complex with substrate OMP at 1.05 Angstroms resolution, 20 minutes soaking

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: G.157, R.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.161, A:R.161 Water bridges: A:G.157 GOL.6: 2 residues within 4Å: Chain B: G.157, R.161 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.157, B:R.161, B:R.161

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

SO4.2: 2 residues within 4Å: Chain A: N.210, R.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.210 Water bridges: A:Q.208 Salt bridges: A:R.219 SO4.3: 2 residues within 4Å: Chain A: T.151, G.206 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.151, A:T.151 Water bridges: A:D.203, A:G.206, A:G.206, B:K.129 SO4.7: 2 residues within 4Å: Chain B: T.151, G.206 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.151, B:T.151 Water bridges: B:G.206, B:G.206 SO4.8: 2 residues within 4Å: Chain B: N.210, R.219 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.210 Water bridges: B:Q.208 Salt bridges: B:R.219

1 x OMP: OROTIDINE-5'-MONOPHOSPHATE(Non-covalent)

OMP.4: 20 residues within 4Å: Chain A: S.34, D.36, K.58, H.60, D.89, K.91, N.118, M.148, S.149, I.178, P.194, Q.207, Y.209, I.225, G.227, R.228 Chain B: D.94, I.95, T.98 Ligands: U.5 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.178, A:P.194 Hydrogen bonds: A:S.34, A:D.36, A:K.58, A:N.118, A:S.149, A:S.149, A:S.149, A:Q.207, A:Y.209, A:Y.209, A:Y.209, A:G.227, A:R.228, B:T.98, B:T.98 Water bridges: A:G.195, A:G.195, A:Q.197, A:G.229 Salt bridges: A:K.58, A:R.228

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

U.5: 17 residues within 4Å: Chain A: S.34, D.36, K.58, H.60, D.89, K.91, M.148, S.149, P.194, Q.207, Y.209, G.227, R.228 Chain B: D.94, I.95, T.98 Ligands: OMP.4 37 PLIP interactions: 19 interactions with chain B, 18 interactions with chain A Hydrophobic interactions: B:I.178, B:P.194, A:P.194 Hydrogen bonds: B:S.34, B:D.36, B:K.58, B:T.98, B:T.98, B:S.149, B:S.149, B:S.149, B:Q.207, B:Y.209, B:Y.209, B:G.227, B:R.228, A:S.34, A:D.36, A:K.58, A:T.98, A:S.149, A:S.149, A:S.149, A:Q.207, A:Y.209, A:Y.209, A:Y.209, A:G.227, A:R.228 Water bridges: B:G.195, B:G.195, B:Q.197, A:G.195, A:G.195, A:Q.197 Salt bridges: B:R.228, A:R.228 U.9: 18 residues within 4Å: Chain A: D.94, I.95, T.98 Chain B: S.34, D.36, K.58, H.60, D.89, K.91, M.148, S.149, I.178, P.194, Q.207, Y.209, V.226, G.227, R.228 Protein-ligand interaction information (PLIP) not available

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

2022-04-13

Peptides

Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine 5'-monophosphate synthase

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