SMTL ID : 7em6.1

Crystal structure of the PI5P4Kbeta N203D-ITP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

2 x IDP: INOSINE-5'-DIPHOSPHATE(Non-covalent)

IDP.1: 11 residues within 4Å: Chain A: F.116, V.125, D.180, V.181, F.182, K.191, D.193, T.214, L.259, I.345, D.346 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.180, A:V.181, A:K.191, A:D.193, A:T.214, A:T.214, A:D.346, A:D.346 IDP.3: 11 residues within 4Å: Chain B: F.116, V.125, K.127, D.180, V.181, F.182, D.193, S.257, L.259, I.345, D.346 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.180, B:V.181, B:D.193, B:D.193, B:S.257, B:D.346 Salt bridges: B:K.127, B:K.127

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

CZU.2: 10 residues within 4Å: Chain A: K.49, K.73, Y.75, S.131, V.134, A.135, H.138, R.165, E.172, Y.174 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.75 Salt bridges: 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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