SMTL ID : 5w25.3 (2 other biounits)

Crystal structure of Aspartyl-tRNA synthetase from Mycobacterium tuberculosis complexed with L-Aspartic Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 13 residues within 4Å: Chain A: E.195, S.217, Q.219, K.222, R.241, Q.255, H.473, H.474, G.510, G.511, R.514, I.556, A.557 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.557 Hydrogen bonds: A:E.195, A:S.217, A:Q.255, D.1 Salt bridges: A:K.222, A:R.241, A:H.473, A:H.473, A:H.474, A:R.514 ASP.5: 14 residues within 4Å: Chain B: E.195, S.217, Q.219, K.222, R.241, Q.255, H.473, H.474, G.510, G.511, R.514, G.555, I.556, A.557 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.557 Hydrogen bonds: B:E.195, B:S.217, B:Q.255, B:I.556, D.5 Salt bridges: B:K.222, B:R.241, B:H.473, B:H.473, B:H.474, B:R.514

3 x LYS: LYSINE(Non-covalent)

LYS.2: 5 residues within 4Å: Chain A: R.25, S.26 Chain B: R.232, F.262, V.263 7 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: B:R.232, K.2, K.2, A:R.25 Salt bridges: B:R.232, A:R.25 Hydrophobic interactions: A:R.25 LYS.3: 7 residues within 4Å: Chain A: D.180, E.231, R.232 Chain B: R.25, A.64 Ligands: LYS.6, GLU.7 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:A.64 Salt bridges: B:R.25, A:R.232, K.6 Hydrogen bonds: A:D.180, E.7 LYS.6: 5 residues within 4Å: Chain A: R.232, F.262 Chain B: R.25, A.28 Ligands: LYS.3 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:R.25 Hydrogen bonds: B:R.25, K.3 Salt bridges: B:R.25, A:R.232 Water bridges: A:R.232

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 3 residues within 4Å: Chain A: A.64, S.65, D.156 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: E.4, E.4 GLU.7: 3 residues within 4Å: Chain B: S.65, D.156 Ligands: LYS.3 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Salt bridges: K.3 Hydrogen bonds: B:D.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal structure of Aspartyl-tRNA synthetase from Mycobacterium tuberculosis complexed with L-Aspartic Acid. to be published

Release Date

2017-06-14

Peptides

Aspartate--tRNA(Asp/Asn) ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate--tRNA(Asp/Asn) ligase

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