SMTL ID : 7f0n.1

Structure of deamidated Ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

10 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: E.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.64 NA.2: 1 residues within 4Å: Chain A: D.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.58 Water bridges: A:T.55, A:T.55 NA.3: 3 residues within 4Å: Chain A: E.51, D.52, G.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.53 NA.4: 3 residues within 4Å: Chain A: P.19, S.20, S.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.57, A:S.57 Water bridges: A:S.20 NA.5: 3 residues within 4Å: Chain A: E.24, D.52, G.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.24 NA.6: 1 residues within 4Å: Chain A: D.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.32 NA.7: 3 residues within 4Å: Chain A: Q.2, F.4, E.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.64 NA.8: 1 residues within 4Å: Chain A: E.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.64 NA.9: 1 residues within 4Å: Chain A: K.48 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.48, A:K.48 NA.10: 3 residues within 4Å: Chain A: A.28, Q.31, D.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.28 Water bridges: A:D.32

1 x K: POTASSIUM ION(Non-covalent)

K.11: 3 residues within 4Å: Chain A: E.64, S.65, T.66 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.64, A:T.66, H2O.4

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain A: R.74, G.75, G.76 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.74, A:G.75, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rashmi, R. et al., Structure of deamidated Ubiquitin. To Be Published

Release Date

2022-06-08

Peptides

Ubiquitin-40S ribosomal protein S27a: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin-40S ribosomal protein S27a