SMTL ID : 7em5.1

Crystal structure of the PI5P4Kbeta F205L-XTP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x CZC: [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate(Non-covalent)

CZC.1: 10 residues within 4Å: Chain A: F.116, V.125, N.180, V.181, L.182, K.191, T.214, L.259, I.345, D.346 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.180, A:V.181, A:T.214, A:D.346 Water bridges: A:N.180 CZC.3: 10 residues within 4Å: Chain B: F.116, V.125, K.127, N.180, V.181, L.182, T.214, L.259, I.345, D.346 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.180, B:V.181 Salt bridges: B:K.127, B:K.127

1 x CZF: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

CZF.2: 9 residues within 4Å: Chain A: K.73, Y.75, S.131, V.134, A.135, H.138, R.165, E.172, Y.174 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.75, A:Y.75, A:E.172, A:E.172 Salt bridges: A:K.53, A:K.73, A:K.73, A:R.165, A:R.165, A:R.165 pi-Stacking: A:H.138, A:H.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeuchi, K. et al., The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure (2022)

Release Date

2022-03-30

Peptides

Phosphatidylinositol 5-phosphate 4-kinase type-2 beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

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