SMTL ID : 7asq.1

Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the reaction product UMP at 0.95 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.95 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: K.20, I.77, A.80, K.81, E.84, F.85, L.86, I.87, D.116 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.20, A:A.80, A:F.85, A:I.87 Water bridges: A:D.116 GOL.6: 10 residues within 4Å: Chain B: K.20, I.77, A.80, K.81, E.84, F.85, L.86, I.87, D.116 Ligands: SO4.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.20, B:A.80, B:F.85, B:I.87 Water bridges: B:D.116

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.2: 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 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.195 Hydrogen bonds: A:S.35, A:D.37, A:K.59, A:H.61, A:S.150, A:S.150, A:Q.208, A:Y.210, A:G.228, A:R.229, B:D.95, B:T.99 Water bridges: A:G.196, A:V.197, A:Q.198, A:R.229 Salt bridges: A:R.229 U5P.7: 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 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.195 Hydrogen bonds: B:S.35, B:K.59, B:H.61, B:S.150, B:S.150, B:Q.208, B:Y.210, B:G.228, B:R.229, A:D.95, A:T.99 Water bridges: B:G.196, B:V.197, B:Q.198, B:R.229 Salt bridges: B:R.229

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

SO4.3: 4 residues within 4Å: Chain A: E.29, R.245, K.246, W.249 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.29 Water bridges: A:R.245, A:R.245, A:R.245, A:R.245 Salt bridges: A:R.245 SO4.4: 6 residues within 4Å: Chain A: I.77, K.81, S.113, W.114, R.141 Ligands: GOL.1 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.141, A:R.141, A:R.141 Salt bridges: A:K.81, A:R.141 SO4.8: 4 residues within 4Å: Chain B: E.29, R.245, K.246, W.249 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.245, B:R.245, B:R.245, B:R.245 Salt bridges: B:R.245 SO4.9: 6 residues within 4Å: Chain B: I.77, K.81, S.113, W.114, R.141 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.141, B:R.141, B:R.141 Salt bridges: B:K.81, B:R.141

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: T.30, N.31, L.32, R.245, A.248, W.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.30, A:N.31, A:W.249 NA.10: 6 residues within 4Å: Chain B: T.30, N.31, L.32, R.245, A.248, W.249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.31, B:R.245, B:W.249

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

2021-11-24

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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