SMTL ID : 7c1y.1

Pseudouridine and ADP bound structure of Pseudouridine kinase (PUKI) from Arabidopsis thaliana

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: K.305, A.341, V.342, S.344, D.346 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.305, A:A.341 NA.4: 4 residues within 4Å: Chain B: K.305, A.341, S.344, D.346 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.344, B:S.344

2 x FJF: 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione(Non-covalent)

FJF.2: 16 residues within 4Å: Chain A: I.10, D.12, G.36, G.37, V.38, N.41, V.90, A.105, N.137, V.162, K.166, T.307, G.308, D.311, N.347 Chain B: T.26 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Water bridges: B:T.26, B:T.26, A:G.308, A:D.311 Hydrogen bonds: A:G.37, A:V.38, A:N.41, A:N.137, A:N.137, A:G.308 FJF.5: 14 residues within 4Å: Chain B: I.10, D.12, G.36, G.37, V.38, N.41, V.107, N.137, V.162, K.166, T.307, G.308, D.311, N.347 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.10 Hydrogen bonds: B:G.37, B:V.38, B:N.41, B:N.137, B:N.137

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 17 residues within 4Å: Chain A: N.183, T.237, L.238, G.239, S.240, G.242, T.298, I.299, A.301, V.303, L.306, A.309, G.310, L.313, I.335, A.338, V.342 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.183, A:T.237, A:L.238, A:G.239, A:G.310 Water bridges: A:A.301, A:G.308, A:D.311 ADP.6: 16 residues within 4Å: Chain B: N.183, T.237, L.238, G.239, S.240, G.242, T.298, I.299, A.301, V.303, A.309, G.310, L.313, I.335, A.338, V.342 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.183, B:T.237, B:T.237, B:L.238, B:G.239, B:T.298, B:G.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S.H. et al., Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana. Nucleic Acids Res. (2021)

Release Date

2020-11-18

Peptides

PfkB-like carbohydrate kinase family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PfkB-like carbohydrate kinase family protein

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