SMTL ID : 7brd.1 (1 other biounit)

Crystal structure of Peptidyl-tRNA hydrolase from Klebsiella pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 6 residues within 4Å: Chain A: E.42, K.44, R.51, R.60, F.81, Y.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.42, A:R.60, A:Y.82 Water bridges: A:R.51

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 2 residues within 4Å: Chain A: R.34, H.35 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain A: R.51, I.52, N.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.53 Water bridges: A:H.35, A:R.51 EDO.4: 2 residues within 4Å: Chain A: S.157, E.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.157, A:E.158 EDO.9: 4 residues within 4Å: Chain A: D.97, L.98, K.104, R.134 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.97, A:R.134, A:R.134 Water bridges: A:K.104 EDO.10: 2 residues within 4Å: Chain A: P.155, A.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.156

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

ACT.5: 2 residues within 4Å: Chain A: E.41, Y.48 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.48 ACT.6: 3 residues within 4Å: Chain A: G.13, A.14, E.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.14 Hydrogen bonds: A:A.14, A:E.15 ACT.7: 3 residues within 4Å: Chain A: K.106, G.109, G.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.110 Salt bridges: A:K.106 ACT.8: 3 residues within 4Å: Chain A: W.26, Q.159, D.163 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.26 Hydrogen bonds: A:Q.159, A:D.163 ACT.11: 3 residues within 4Å: Chain A: R.20, F.149, K.153 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.20 ACT.12: 1 residues within 4Å: Chain A: R.34 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.34 ACT.19: 1 residues within 4Å: Ligands: SO4.18 No protein-ligand interaction detected (PLIP)

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

CL.13: 3 residues within 4Å: Chain A: N.11, H.21, N.115 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: K.145, G.148 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: P.100, I.137, G.138, F.149, E.158 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: H.93, E.95, G.110 Ligand excluded by PLIP

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

SO4.17: 2 residues within 4Å: Chain A: R.171, R.187 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.171, A:R.187 SO4.18: 4 residues within 4Å: Chain A: E.41, E.42, S.43 Ligands: ACT.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.43 Water bridges: A:S.43, A:S.43, A:K.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mundra, S. et al., Structural and functional characterization of peptidyl-tRNA hydrolase from Klebsiella pneumoniae. Biochim Biophys Acta Proteins Proteom (2021)

Release Date

2021-03-17

Peptides

Peptidyl-tRNA hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidyl-tRNA hydrolase

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