SMTL ID : 4r2m.1

Crystal Structure of R134D mutant of YnaF (Universal Stress Protein F) from Salmonella typhimurium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.131, N.142 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: R.131, N.142 Ligands: ANP.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: R.131, N.142 Ligands: ANP.6 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain D: R.131, N.142 Ligands: ANP.8 No protein-ligand interaction detected (PLIP)

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 24 residues within 4Å: Chain A: P.22, I.23, D.24, L.30, L.52, T.53, V.54, P.109, I.113, I.127, A.128, H.130, R.131, T.135, Y.137, G.140, S.141, N.142, A.143 Chain C: Y.60, S.108, K.110, D.111 Ligands: MG.1 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:V.54, A:V.54, A:A.128, A:R.131, A:T.135, A:S.141, A:A.143, C:S.108, C:K.110, C:K.110 Water bridges: A:P.22, A:P.22, A:D.24, A:R.131, A:R.131, A:R.131, A:R.131, A:R.131, A:N.142, A:N.142, A:N.142, A:N.142 Salt bridges: A:H.130, A:R.131 ANP.4: 20 residues within 4Å: Chain B: P.22, I.23, D.24, L.52, T.53, V.54, P.109, I.113, I.127, A.128, H.130, R.131, G.140, S.141, N.142, A.143 Chain D: Y.60, K.110, D.111 Ligands: MG.3 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:D.24, B:T.53, B:V.54, B:V.54, B:A.128, B:R.131, B:R.131, B:S.141, B:A.143, D:K.110, D:K.110, D:D.111 Water bridges: B:P.22, B:P.22, B:D.24, B:D.24, B:R.131, B:R.131, B:R.131, B:N.142, B:N.142 Salt bridges: B:H.130, B:R.131 ANP.6: 24 residues within 4Å: Chain A: Y.60, S.108, K.110, D.111 Chain C: P.22, I.23, D.24, L.30, L.52, T.53, V.54, P.109, I.113, I.127, A.128, H.130, R.131, T.135, Y.137, G.140, S.141, N.142, A.143 Ligands: MG.5 26 PLIP interactions: 23 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:D.24, C:V.54, C:V.54, C:A.128, C:R.131, C:T.135, C:T.135, C:S.141, C:A.143, A:S.108, A:K.110, A:K.110 Water bridges: C:P.22, C:P.22, C:D.24, C:R.131, C:R.131, C:R.131, C:R.131, C:R.131, C:N.142, C:N.142, C:N.142, C:N.142 Salt bridges: C:H.130, C:R.131 ANP.8: 20 residues within 4Å: Chain B: Y.60, K.110, D.111 Chain D: P.22, I.23, D.24, L.52, T.53, V.54, P.109, I.113, I.127, A.128, H.130, R.131, G.140, S.141, N.142, A.143 Ligands: MG.7 21 PLIP interactions: 3 interactions with chain B, 18 interactions with chain D Hydrogen bonds: B:K.110, B:K.110, B:D.111, D:V.54, D:V.54, D:A.128, D:R.131, D:R.131, D:S.141, D:A.143 Water bridges: D:P.22, D:P.22, D:D.24, D:D.24, D:R.131, D:R.131, D:R.131, D:N.142, D:N.142 Salt bridges: D:H.130, D:R.131

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 F: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Universal stress protein F