SMTL ID : 7n6s.1 (1 other biounit)

Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E in complex with 2'-deoxyuridine 5'-monophoephate (dUMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

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

UMP.1: 14 residues within 4Å: Chain A: I.69, N.85, G.88, T.89, I.90, D.91, Y.94, E.97, I.98, K.99 Chain B: R.72, S.73, Q.120 Chain C: R.142 20 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C, 11 interactions with chain A Hydrogen bonds: B:S.73, B:S.73, B:Q.120, C:R.142, A:N.85, A:T.89, A:D.91, A:D.91, A:Y.94, A:K.99, A:K.99 Water bridges: B:P.71, B:G.74, B:G.74, B:Q.120, C:R.142, A:T.89, A:T.89 Hydrophobic interactions: A:I.90, A:Y.94 UMP.2: 11 residues within 4Å: Chain B: I.69, N.85, G.88, T.89, I.90, Y.94, E.97, I.98, K.99 Chain C: R.72, S.73 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:Y.94 Hydrogen bonds: B:N.85, B:Y.94, B:K.99, B:K.99, C:S.73, C:S.73, C:Q.120 Water bridges: B:T.89, B:T.89, C:S.73, C:G.74, C:Q.120 UMP.3: 14 residues within 4Å: Chain A: R.72, S.73, Q.120 Chain B: R.142 Chain C: I.69, N.85, G.88, T.89, I.90, D.91, Y.94, E.97, I.98, K.99 18 PLIP interactions: 11 interactions with chain C, 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:I.90, C:Y.94 Hydrogen bonds: C:N.85, C:T.89, C:D.91, C:D.91, C:Y.94, C:K.99, C:K.99, A:S.73, A:S.73, A:Q.120 Water bridges: C:T.89, C:T.89, A:R.72, A:R.72, A:Q.120, B:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E in complex with 2'-deoxyuridine 5'-monophoephate (dUMP). to be published

Release Date

2021-06-23

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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