SMTL ID : 3rac.1

Crystal Structure of Histidine--tRNA ligase subunit from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.1: 14 residues within 4Å: Chain A: E.98, T.100, Y.122, Q.148, E.152, L.311, Y.313, Y.314, Q.332, G.333, Y.336, G.351, F.352, A.353 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.353 Hydrogen bonds: A:T.100, A:T.100, A:Q.148, A:Y.313, A:Q.332, A:Y.336 Water bridges: A:M.99, A:T.100, A:R.309, A:R.309 LMR.7: 14 residues within 4Å: Chain B: E.98, T.100, Y.122, Q.148, E.152, L.311, Y.313, Y.314, Q.332, G.333, Y.336, G.351, F.352, A.353 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.353 Hydrogen bonds: B:E.98, B:T.100, B:T.100, B:Y.122, B:Q.148, B:Y.314, B:Q.332 Water bridges: B:M.99, B:T.100, B:R.309, B:R.309

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

NA.2: 4 residues within 4Å: Chain A: S.187, V.192, L.305, L.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.187, A:L.307 NA.3: 4 residues within 4Å: Chain A: V.59, Y.122, C.123, E.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.123, A:E.124, A:E.124 NA.8: 4 residues within 4Å: Chain B: S.187, V.192, L.305, L.307 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.187, B:L.305 NA.9: 4 residues within 4Å: Chain B: V.59, Y.122, C.123, E.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.123, B:E.124 Water bridges: B:T.60

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 3 residues within 4Å: Chain A: R.125 Chain B: R.125 Ligands: ACY.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:R.41, A:R.41 Salt bridges: B:R.125, A:R.125 ACY.5: 6 residues within 4Å: Chain A: R.72, A.73, R.74, S.75, D.312, Y.313 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.312, A:Y.313 Hydrogen bonds: A:A.73 ACY.10: 3 residues within 4Å: Chain A: R.125 Chain B: R.125 Ligands: ACY.4 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:R.41, A:R.41 Salt bridges: B:R.125, A:R.125 ACY.11: 6 residues within 4Å: Chain B: R.72, A.73, R.74, S.75, D.312, Y.313 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.312, B:Y.313 Hydrogen bonds: B:A.73

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: Q.30, F.36, R.40, E.145 Chain B: T.60 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.32, A:R.40, A:R.40, A:E.145, A:E.357 Water bridges: A:Q.30 GOL.12: 5 residues within 4Å: Chain A: T.60 Chain B: Q.30, F.36, R.40, E.145 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.32, B:R.40, B:R.40, B:E.145, B:E.145 Water bridges: B:Q.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., Crystal Strucutre of Histidine--tRNA ligase subunit from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446. To be Published

Release Date

2011-09-14

Peptides

Histidine-tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histidine-tRNA ligase