SMTL ID : 6kz6.1

Crystal structure of ASFV dUTPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-trimer

Ligands

3 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 12 residues within 4Å: Chain A: N.106, G.109, L.110, I.111, D.112, Y.115, E.118, L.119, M.120 Chain C: R.92, S.93 Ligands: MG.5 21 PLIP interactions: 14 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:S.93, A:N.106, A:L.110, A:D.112, A:M.120, A:M.120 Water bridges: C:A.91, C:R.92, C:S.93, C:S.93, C:S.93, C:S.93, C:S.94, C:Q.141, C:Q.141, C:Q.141, C:Q.141, C:Q.141, A:K.122 Salt bridges: C:R.92 Hydrophobic interactions: A:Y.115 UMP.3: 11 residues within 4Å: Chain A: R.92, S.93 Chain B: N.106, G.109, L.110, I.111, D.112, Y.115, L.119, M.120 Ligands: MG.2 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.111, B:Y.115 Hydrogen bonds: B:N.106, B:L.110, B:D.112, B:D.112, B:M.120, B:M.120, A:S.93 Water bridges: B:K.122, A:R.92, A:S.93, A:Q.141, A:Q.141, A:Q.141 Salt bridges: A:R.92 UMP.4: 7 residues within 4Å: Chain B: S.93 Chain C: I.111, D.112, Y.115, L.119, M.120, K.122 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain C Water bridges: B:S.93, B:S.93, C:N.106 Hydrophobic interactions: C:I.111, C:Y.115 Hydrogen bonds: C:D.112, C:M.120, C:M.120 Salt bridges: C:K.122

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: D.112 Ligands: UMP.3 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: D.54 Ligands: UMP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, G. et al., Structural Insight into African Swine Fever Virus dUTPase Reveals a Novel Folding Pattern in the dUTPase Family. J.Virol. (2020)

Release Date

2019-11-13

Peptides

E165R: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

E165R