SMTL ID : 7ov0.1

Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in resting state at 0.95 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.95 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 14 residues within 4Å: Chain A: S.35, D.37, K.59, H.61, D.90, K.92, P.195, Q.208, I.226, G.228 Chain B: D.95, I.96, T.99 Ligands: SO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.35, A:D.37, A:K.59, A:H.61, A:D.90, A:K.92 Water bridges: A:R.229 GOL.2: 8 residues within 4Å: Chain A: Q.198, L.199, E.200, G.230, I.231, A.234, Y.244 Ligands: PRO.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.198, A:L.199, A:E.200, A:G.230, A:G.230, A:Y.244 GOL.7: 14 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, P.195, Q.208, I.226, G.228 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.35, B:D.37, B:K.59, B:H.61, B:K.92 Water bridges: B:R.229 GOL.8: 8 residues within 4Å: Chain B: Q.198, L.199, E.200, G.230, I.231, A.234, Y.244 Ligands: PRO.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.198, B:L.199, B:E.200, B:G.230, B:G.230, B:Y.244

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

SO4.3: 9 residues within 4Å: Chain A: Q.198, Q.208, Y.210, V.227, G.228, R.229, G.230 Chain B: I.96 Ligands: GOL.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.198, A:Q.208, A:Y.210, A:G.228, A:R.229 Water bridges: A:V.197, A:V.197, A:G.230 Salt bridges: A:R.229 SO4.9: 9 residues within 4Å: Chain A: I.96 Chain B: Q.198, Q.208, Y.210, V.227, G.228, R.229, G.230 Ligands: GOL.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.198, B:Q.208, B:Y.210, B:G.228, B:R.229 Water bridges: B:V.197, B:V.197, B:G.230 Salt bridges: B:R.229

6 x PRO: PROLINE(Non-covalent)

PRO.4: 7 residues within 4Å: Chain A: Q.198, E.200, A.201, G.202, G.203, Y.210 Ligands: GOL.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.210 Hydrogen bonds: A:A.201, A:G.203, P.4 Water bridges: A:A.201 PRO.5: 4 residues within 4Å: Chain A: L.199, E.200, A.201, S.212 3 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: P.5, P.5 Water bridges: A:S.212 PRO.6: 4 residues within 4Å: Chain A: S.4, L.256, G.257, V.258 4 PLIP interactions: 3 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: P.6, P.6, P.6, A:V.258 PRO.10: 7 residues within 4Å: Chain B: Q.198, E.200, A.201, G.202, G.203, Y.210 Ligands: GOL.8 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B Hydrogen bonds: P.10, B:A.201, B:G.203 Hydrophobic interactions: B:Y.210 Water bridges: B:A.201 PRO.11: 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.11, P.11 PRO.12: 4 residues within 4Å: Chain B: S.4, L.256, G.257, V.258 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: B:V.258, B:V.258, P.12, P.12, P.12

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

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