SMTL ID : 9grn.1 (3 other biounits)

Crystal structure of the engineered C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 (apo, loop deletion residues 848-918)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

monomer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: F.24, K.25, H.26, K.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.72 Water bridges: A:E.270 GOL.2: 5 residues within 4Å: Chain A: V.45, I.46, R.47, N.48, D.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.45, A:D.51, A:D.51 GOL.3: 4 residues within 4Å: Chain A: L.63, D.64, E.65, K.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.64, A:K.66 GOL.4: 2 residues within 4Å: Chain A: K.82, S.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.262, A:S.262 GOL.5: 3 residues within 4Å: Chain A: K.21, K.23, K.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.21, A:K.111 Water bridges: A:K.23 GOL.6: 4 residues within 4Å: Chain A: Q.130, D.134, P.470, K.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.130, A:D.134 GOL.7: 2 residues within 4Å: Chain A: R.132, F.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.132, A:R.132 GOL.8: 5 residues within 4Å: Chain A: K.21, G.114, E.153, R.154, R.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.21, A:R.154, A:R.155 GOL.9: 3 residues within 4Å: Chain A: L.63, D.64, K.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.74 GOL.10: 5 residues within 4Å: Chain A: R.231, E.234, L.235, Y.238, Q.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.231, A:R.231

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain A: H.118, R.258, C.260, H.303, H.464 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.118, A:C.260, A:H.303, A:H.464 ZN.12: 3 residues within 4Å: Chain A: H.40, K.41, E.42 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.40, A:E.42, A:E.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raia, P. et al., A small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis. Nat Commun (2025)

Release Date

2025-02-26

Peptides

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

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