SMTL ID : 9grn.4 (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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: R.14, R.18, S.291, F.339, C.343, E.346, Y.347, E.391, Y.395 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.14, A:R.18, A:S.291, A:E.346, A:Y.347, A:E.391, A:E.391 GOL.2: 5 residues within 4Å: Chain A: R.231, E.234, L.235, Y.238, Q.327 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.231, A:R.231, A:E.234, A:Q.327

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 8 residues within 4Å: Chain A: A.217, D.340, P.344, R.412, N.413, L.415, P.416, E.417 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.412 ACT.4: 2 residues within 4Å: Chain A: Q.453, D.454 No protein-ligand interaction detected (PLIP) ACT.5: 4 residues within 4Å: Chain A: S.262, E.263, D.264, L.267 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: H.118, 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

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
D

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

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