SMTL ID : 4r2j.1

Crystal structure of YdaA (Universal Stress Protein E) from Salmonella typhimurium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.131, H.133 Ligands: GLC.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.131, A:H.133 ZN.6: 3 residues within 4Å: Chain B: H.131, H.133 Ligands: GLC.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.131, B:H.133

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: R.36, Y.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.93 Salt bridges: A:R.36 PO4.7: 2 residues within 4Å: Chain B: R.36, Y.93 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.93, B:Y.93 Salt bridges: B:R.36

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: E.254, K.255, T.257, H.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.254 Water bridges: A:H.258 EDO.8: 4 residues within 4Å: Chain B: E.254, K.255, T.257, H.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.254 Water bridges: B:H.258

4 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.4: 4 residues within 4Å: Chain A: H.131, H.133, I.140 Ligands: ZN.1 No protein-ligand interaction detected (PLIP) GLC.5: 12 residues within 4Å: Chain A: F.141, T.142, P.143, W.146, R.150, D.304 Chain B: F.141, P.143, W.146, R.150, D.304 Ligands: GLC.10 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.304, A:R.150, A:R.150, A:D.304 Salt bridges: B:R.150, A:R.150 Water bridges: A:D.304 GLC.9: 4 residues within 4Å: Chain B: H.131, H.133, I.140 Ligands: ZN.6 No protein-ligand interaction detected (PLIP) GLC.10: 12 residues within 4Å: Chain A: F.141, P.143, W.146, R.150, D.304 Chain B: F.141, T.142, P.143, W.146, R.150, D.304 Ligands: GLC.5 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.150, B:R.150, B:D.304, A:D.304 Salt bridges: B:R.150, A:R.150 Water bridges: A:D.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bangera, M. et al., Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance. J.Struct.Biol. (2015)

Release Date

2015-02-04

Peptides

Universal stress protein E: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Universal stress protein E