SMTL ID : 6zx2.1

OMPD-domain of human UMPS in complex with 6-carboxamido-UMP at 1.2 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

2 x QRT: [(2~{R},3~{S},4~{R},5~{R})-5-[6-aminocarbonyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

QRT.1: 19 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, V.229, G.230, R.231 Chain B: D.97, I.98, T.101 24 PLIP interactions: 22 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:D.92, A:K.94, 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:D.97, B:T.101 Water bridges: A:G.198, A:G.198, A:G.232 Salt bridges: A:R.231 QRT.4: 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, N.121, M.151, S.152, I.181, P.197, Q.210, Y.212, V.229, G.230, R.231 21 PLIP interactions: 20 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:D.92, B:K.94, 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:D.97 Water bridges: B:G.198, B:G.198, B:G.232 Salt bridges: B:R.231

2 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.5: 3 residues within 4Å: Chain B: G.8, A.9, E.12 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: P.5, P.5

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

SO4.3: 3 residues within 4Å: Chain A: S.128, K.132, H.173 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.128 Water bridges: A:E.172, A:E.172, A:E.172, A:E.172 Salt bridges: A:K.132, A:H.173 SO4.6: 3 residues within 4Å: Chain B: S.128, K.132, H.173 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.128 Water bridges: B:E.172, B:E.172, B:E.172, B:H.173 Salt bridges: B:K.132, B:H.173

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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