SMTL ID : 8u0z.1

CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE DOMAIN OF Coffea arabica UMP SYNTHASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: A.81, E.82, N.85, F.86 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.85 Water bridges: A:R.78, A:E.82, A:N.85, A:N.85 EDO.4: 6 residues within 4Å: Chain A: R.78, I.88, W.115, D.117, R.142 Ligands: EDO.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.78, A:W.115, A:R.142, A:R.142 Water bridges: A:R.78 EDO.5: 5 residues within 4Å: Chain A: P.6, Y.7, G.8, I.27, Y.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.8 EDO.8: 6 residues within 4Å: Chain B: K.93, L.147, M.150, S.151, I.180, P.201 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.93, B:K.93, B:S.151, B:S.151 EDO.9: 5 residues within 4Å: Chain B: P.6, Y.7, G.8, I.27, Y.258 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.8

1 x N: ANY 5'-MONOPHOSPHATE NUCLEOTIDE(Non-covalent)

N.2: 13 residues within 4Å: Chain A: A.36, D.38, K.60, H.62, D.91, K.93, Q.214, Y.216, G.234, R.235 Chain B: D.96, I.97, T.100 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.38, A:K.60, A:K.93, A:Q.214, A:Y.216, A:Y.216, A:Y.216, A:G.234, A:R.235, B:T.100, B:T.100 Water bridges: A:G.202, A:G.236 Salt bridges: A:R.235

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: A.42, L.46, D.68, T.70, D.72, F.73, K.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.70, A:T.70, A:K.76 GOL.6: 9 residues within 4Å: Chain A: D.96, I.97, T.100 Chain B: A.36, D.38, K.60, H.62, D.91 Ligands: GOL.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.60, B:H.62, B:K.93, A:D.96 GOL.7: 8 residues within 4Å: Chain B: G.202, V.203, Y.216, I.232, V.233, G.234, R.235 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.202, B:V.203, B:G.234, B:R.235

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 9 residues within 4Å: Chain B: K.21, R.78, A.81, E.82, N.85, F.86, I.88, W.115, D.117 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.21, B:N.85, B:W.115 Water bridges: B:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hinojosa-Cruz, A. et al., Structural and functional properties of uridine 5'-monophosphate synthase from Coffea arabica. Int.J.Biol.Macromol. (2024)

Release Date

2024-01-17

Peptides

Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine 5'-monophosphate synthase