SMTL ID : 8hyg.1

Crystal structure of protease-associated domain of Arabidopsis vacuolar sorting receptor 1 at pH 4.6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: S.18, I.19, S.141, S.144, A.145 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.145 Hydrogen bonds: A:A.145 ACT.8: 5 residues within 4Å: Chain A: R.78, K.104, E.106, T.110, M.111 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.78, A:K.104 ACT.9: 5 residues within 4Å: Chain A: I.19, Y.23, T.137, L.138, S.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.23, A:S.141 ACT.10: 3 residues within 4Å: Chain A: R.78, F.83, M.111 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.83 Salt bridges: A:R.78

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

PEG.2: 5 residues within 4Å: Chain A: G.1, S.2, R.3, D.112, T.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.3, A:R.3 PEG.5: 2 residues within 4Å: Chain A: S.57, D.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 PEG.6: 4 residues within 4Å: Chain A: K.64, G.94, A.96 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.65, A:G.94 PEG.7: 6 residues within 4Å: Chain A: L.39, P.71, A.96, I.129, P.130 Ligands: PEG.6 No protein-ligand interaction detected (PLIP) PEG.11: 4 residues within 4Å: Chain A: K.54, S.55, D.58 Ligands: EPE.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.55

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

CL.3: 1 residues within 4Å: Chain A: R.3 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 7 residues within 4Å: Chain A: C.53, K.54, S.55, W.88, I.89, Y.123 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsao, H.E. et al., Crystal structure of protease-associated domain of Arabidopsis vacuolar sorting receptor 1 at pH 4.6. To Be Published

Release Date

2023-01-25

Peptides

Vacuolar-sorting receptor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vacuolar-sorting receptor 1

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