SMTL ID : 4r2k.1

Crystal structure of H119A mutant of YdaA (Universal Stress Protein E) from Salmonella typhimurium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: K.128, T.142, T.144 Chain B: Q.301 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.142, A:T.142, A:T.144, B:Q.301 Water bridges: A:K.128, A:K.128, A:T.144, B:Q.301 Salt bridges: A:K.128 SO4.2: 3 residues within 4Å: Chain A: T.72, R.75, Q.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.76 Water bridges: A:T.72, A:R.75 Salt bridges: A:R.75 SO4.3: 5 residues within 4Å: Chain A: E.137, D.304, H.305, R.307 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.304 Water bridges: A:A.138 Salt bridges: A:H.305, A:R.307 SO4.4: 2 residues within 4Å: Chain A: R.236, L.240 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.236 SO4.21: 2 residues within 4Å: Chain A: R.247, Q.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.248 Salt bridges: A:R.247 SO4.22: 3 residues within 4Å: Chain A: P.216, I.217, K.261 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.217 Water bridges: A:N.218, A:K.261, A:K.261 Salt bridges: A:K.261 SO4.24: 3 residues within 4Å: Chain A: H.258, H.274, L.275 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.258, A:H.274 SO4.25: 4 residues within 4Å: Chain A: Q.301 Chain B: K.128, T.142, T.144 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.142, B:T.144, A:Q.301 Water bridges: B:K.128, B:K.128, B:T.144, A:Q.301 Salt bridges: B:K.128 SO4.26: 3 residues within 4Å: Chain B: T.72, R.75, Q.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.76 Water bridges: B:T.72, B:R.75 Salt bridges: B:R.75 SO4.27: 5 residues within 4Å: Chain B: E.137, D.304, H.305, R.307 Ligands: EDO.38 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.304 Water bridges: B:A.138 Salt bridges: B:H.305, B:R.307 SO4.28: 2 residues within 4Å: Chain B: R.236, L.240 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.236 SO4.45: 2 residues within 4Å: Chain B: R.247, Q.248 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.248 Salt bridges: B:R.247 SO4.46: 3 residues within 4Å: Chain B: P.216, I.217, K.261 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.217 Water bridges: B:N.218, B:K.261, B:K.261 Salt bridges: B:K.261 SO4.48: 3 residues within 4Å: Chain B: H.258, H.274, L.275 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.258 Salt bridges: B:H.258, B:H.274

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

EDO.5: 7 residues within 4Å: Chain A: V.214, P.216, L.263, E.266 Chain B: F.58, M.62 Ligands: EDO.32 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: Q.29, D.30, D.31 Ligands: EDO.18 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: R.36, V.39, Y.40, Q.43 Ligands: EDO.10 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: F.58, V.78, R.82 Ligands: EDO.29, EDO.41 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Q.89, A.90, K.91, Y.92, Y.93 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: R.36, Y.93 Ligands: EDO.7 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: F.226, D.227, Y.231 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: V.285, G.286, G.289, P.315, Y.318 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: N.28 Chain B: E.265, E.266, H.305 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: P.269, D.270, H.305, R.307 Ligands: SO4.3 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: D.30, D.31, Q.32, R.36, Q.89, Y.93 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: A.173, P.264, G.283, L.295, T.298, A.299 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: L.263, E.266 Chain B: P.27, N.28, F.58, R.82 Ligands: EDO.32 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: P.27, N.28, Q.29, D.30, R.82, W.85 Ligands: EDO.6 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: Y.212, R.236, K.261 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: S.291, A.292, A.293 Chain B: N.108 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: F.58, M.62 Chain B: V.214, P.216, L.263, E.266 Ligands: EDO.8 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: Q.29, D.30, D.31 Ligands: EDO.42 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: R.36, V.39, Y.40, Q.43 Ligands: EDO.34 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: F.58, V.78, R.82 Ligands: EDO.5, EDO.17 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: Q.89, A.90, K.91, Y.92, Y.93 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: R.36, Y.93 Ligands: EDO.31 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: F.226, D.227, Y.231 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: V.285, G.286, G.289, P.315, Y.318 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain A: E.265, E.266, H.305 Chain B: N.28 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: P.269, D.270, H.305, R.307 Ligands: SO4.27 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain B: D.30, D.31, Q.32, R.36, Q.89, Y.93 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain B: A.173, P.264, G.283, L.295, T.298, A.299 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain A: P.27, N.28, F.58, R.82 Chain B: L.263, E.266 Ligands: EDO.8 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain B: P.27, N.28, Q.29, D.30, R.82, W.85 Ligands: EDO.30 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: Y.212, R.236, K.261 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain A: N.108 Chain B: S.291, A.292, A.293 Ligand excluded by PLIP

2 x OXD: OXALIC ACID(Non-covalent)

OXD.23: 6 residues within 4Å: Chain A: H.147, R.150, K.151 Chain B: R.150, K.151 Ligands: OXD.47 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Salt bridges: A:H.147, A:R.150, A:K.151, A:K.151, B:H.147, B:R.150, B:K.151, B:K.151 OXD.47: 6 residues within 4Å: Chain A: R.150, K.151 Chain B: H.147, R.150, K.151 Ligands: OXD.23 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Salt bridges: A:H.147, A:R.150, A:K.151, A:K.151, B:H.147, B:R.150, B:K.151, B:K.151

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