SMTL ID : 9e4v.1

The structure of human vacuolar protein sorting 34 catalytic domain bound to MES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

monomer

Ligands

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 12 residues within 4Å: Chain A: I.357, K.359, Y.393, M.405, Q.406, F.407, I.408, S.410, L.473, I.483, D.484 Ligands: PG4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.408, A:D.484

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 13 residues within 4Å: Chain A: F.335, S.337, P.341, I.357, K.359, F.407, I.408, S.410, V.411, P.412, L.473, I.483 Ligands: MES.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.337, A:S.410

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: K.336, S.337, A.338, M.340 No protein-ligand interaction detected (PLIP)

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: R.289, T.333, L.334, F.335, K.336, Q.343, F.407 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.333, A:K.336, A:Q.343 PEG.5: 6 residues within 4Å: Chain A: Q.409, S.410, V.411, T.475, K.476, T.477 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.409 Hydrogen bonds: A:K.476, A:T.477 PEG.11: 4 residues within 4Å: Chain A: I.221, C.224, L.241, M.244 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.221 PEG.12: 3 residues within 4Å: Chain A: E.129, N.130, F.131 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: S.263, L.264, A.267, E.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.263, A:E.312 Water bridges: A:E.312

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: Y.33, E.34 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.101, E.129 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: P.65, Q.66 Ligand excluded by PLIP

3 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.14: 1 residues within 4Å: Chain A: S.210 No protein-ligand interaction detected (PLIP) K.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abiodun, W.O. et al., Facile Bacterial Production of Human Vacuolar Protein Sorting 34 Enables Structural Characterization of Novel Inhibitors. To Be Published

Release Date

2024-11-06

Peptides

Phosphatidylinositol 3-kinase catalytic subunit type 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphatidylinositol 3-kinase catalytic subunit type 3