SMTL ID : 3r3q.1

Crystal structure of the yeast Vps23 UEV domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: D.160 Ligands: IMD.19 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.160, A:D.160, H2O.4 ZN.2: 2 residues within 4Å: Chain A: E.13 Ligands: IMD.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.13, A:E.13, H2O.3 ZN.3: 3 residues within 4Å: Chain A: H.35 Ligands: IMD.11, ACT.18 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.35 ZN.4: 2 residues within 4Å: Chain A: D.76 Ligands: IMD.12 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.76, H2O.3 ZN.5: 2 residues within 4Å: Chain A: E.120, E.156 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.120, A:E.156, A:E.156, H2O.4 ZN.6: 3 residues within 4Å: Chain A: E.75 Ligands: CL.10, IMD.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.75, A:E.75 ZN.7: 3 residues within 4Å: Chain A: H.155 Ligands: IMD.15, ACT.16 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.155 ZN.8: 4 residues within 4Å: Chain A: D.29, T.32 Ligands: ACT.17, IMD.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.29, A:D.29, A:T.32 ZN.9: 2 residues within 4Å: Chain A: D.42 Ligands: IMD.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.42, H2O.3, H2O.4

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

CL.10: 7 residues within 4Å: Chain A: E.75, P.80, I.112, S.113, L.116 Ligands: ZN.6, IMD.13 Ligand excluded by PLIP

7 x IMD: IMIDAZOLE(Non-covalent)

IMD.11: 7 residues within 4Å: Chain A: H.35, L.38, A.39, D.42 Ligands: ZN.3, ZN.9, ACT.18 No protein-ligand interaction detected (PLIP) IMD.12: 2 residues within 4Å: Chain A: D.76 Ligands: ZN.4 No protein-ligand interaction detected (PLIP) IMD.13: 8 residues within 4Å: Chain A: E.75, S.113, S.115, L.116 Ligands: ZN.6, CL.10, IMD.15, ACT.16 No protein-ligand interaction detected (PLIP) IMD.14: 2 residues within 4Å: Chain A: E.13 Ligands: ZN.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.17 IMD.15: 5 residues within 4Å: Chain A: E.75, H.155 Ligands: ZN.7, IMD.13, ACT.16 No protein-ligand interaction detected (PLIP) IMD.19: 2 residues within 4Å: Chain A: D.160 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.160 IMD.20: 4 residues within 4Å: Chain A: D.29, T.32 Ligands: ZN.8, ACT.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.29, A:T.32

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

ACT.16: 6 residues within 4Å: Chain A: S.115, H.155, E.156 Ligands: ZN.7, IMD.13, IMD.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.156 Salt bridges: A:H.155 ACT.17: 4 residues within 4Å: Chain A: D.29, T.32 Ligands: ZN.8, IMD.20 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.31 ACT.18: 3 residues within 4Å: Chain A: H.35 Ligands: ZN.3, IMD.11 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.35 ACT.21: 1 residues within 4Å: Chain A: H.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, X. et al., Structural basis for endosomal recruitment of ESCRT-I by ESCRT-0 in yeast. Embo J. (2011)

Release Date

2011-05-04

Peptides

Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease

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