SMTL ID : 9grn.2 (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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: K.53, L.56, Q.57, R.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.53, A:Q.57, A:R.60 GOL.2: 5 residues within 4Å: Chain A: K.25, S.27, V.96, K.105, Q.107 No protein-ligand interaction detected (PLIP) GOL.3: 7 residues within 4Å: Chain A: E.126, L.460, D.461, R.463, Y.465, S.467 Ligands: LPC.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126, A:D.461, A:R.463, A:Y.465 GOL.5: 8 residues within 4Å: Chain A: Q.256, R.258, R.305, Q.306, L.460, D.461, D.462, H.464 No protein-ligand interaction detected (PLIP) GOL.6: 2 residues within 4Å: Chain A: E.208, E.224 No protein-ligand interaction detected (PLIP)

1 x LPC: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE(Non-covalent)

LPC.4: 6 residues within 4Å: Chain A: E.126, E.129, Q.130, S.467, C.468 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.126

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 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 ZN.8: 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
B

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

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