SMTL ID : 6yvm.1

Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 2.13 MGy exposure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

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

OMP.1: 21 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, D.92, K.94, N.121, M.151, S.152, I.181, P.197, Q.210, Y.212, I.228, V.229, G.230, R.231 Chain B: D.97, I.98, T.101 Ligands: U.2 23 PLIP interactions: 21 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:N.121, 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:K.61, A:R.231 OMP.10: 21 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, N.121, M.151, S.152, I.181, P.197, Q.210, Y.212, I.228, V.229, G.230, R.231 Ligands: U.11 20 PLIP interactions: 19 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:N.121, 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:K.61, B:R.231

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

U.2: 19 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, I.228, G.230, R.231 Chain B: D.97, I.98, T.101 Ligands: OMP.1 40 PLIP interactions: 21 interactions with chain A, 19 interactions with chain B Hydrophobic interactions: A:I.181, A:P.197, B:I.181, B:P.197 Hydrogen bonds: A:S.37, A:D.39, A:D.39, A:K.61, A:D.92, A:T.101, 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:S.37, B:D.39, B:K.61, B:T.101, B:T.101, B:S.152, B:S.152, B:S.152, B:Q.210, B:Y.212, B:Y.212, B:G.230, B:R.231 Water bridges: A:G.198, A:G.198, A:Q.200, B:G.198, B:G.198, B:Q.200 Salt bridges: A:R.231, B:R.231 U.11: 19 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, I.228, G.230, R.231 Ligands: OMP.10 Protein-ligand interaction information (PLIP) not available

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: R.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.191, A:E.191 GOL.12: 1 residues within 4Å: Chain B: R.15 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.191, B:E.191

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

SO4.4: 2 residues within 4Å: Chain A: T.154, G.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.154 Water bridges: A:G.209, A:G.209 SO4.5: 2 residues within 4Å: Chain A: R.15, E.175 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.15 Salt bridges: A:R.15 SO4.6: 2 residues within 4Å: Chain A: N.213, R.222 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.213, A:N.213 Water bridges: A:Q.211, A:Q.211 Salt bridges: A:R.222 SO4.7: 2 residues within 4Å: Chain A: G.160, R.164 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.160 Salt bridges: A:R.164 SO4.8: 3 residues within 4Å: Chain A: S.128, K.132, H.173 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.128 Water bridges: A:E.172, A:E.172 Salt bridges: A:K.132, A:H.173 SO4.9: 2 residues within 4Å: Chain A: R.164, R.168 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.164, A:R.168, A:R.168 Salt bridges: A:R.168 SO4.13: 2 residues within 4Å: Chain B: T.154, G.209 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.154, B:T.154 Water bridges: B:G.209, B:G.209 SO4.14: 2 residues within 4Å: Chain B: R.15, E.175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.175 Water bridges: B:R.15 Salt bridges: B:R.15 SO4.15: 2 residues within 4Å: Chain B: N.213, R.222 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.213, B:N.213 Water bridges: B:Q.211, B:Q.211 Salt bridges: B:R.222 SO4.16: 2 residues within 4Å: Chain B: G.160, R.164 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.160 Salt bridges: B:R.164 SO4.17: 3 residues within 4Å: Chain B: S.128, K.132, H.173 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.128 Water bridges: B:E.172, B:H.173 Salt bridges: B:K.132, B:H.173 SO4.18: 2 residues within 4Å: Chain B: R.164, R.168 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.164, B:R.168, B:R.168 Salt bridges: B:R.168

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

2021-11-17

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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