SMTL ID : 3tzl.1

Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni complexed with ADP and Tryptophane

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: Q.11, H.17, G.19, N.20, G.23, A.24, A.183, V.184, V.185, K.192, M.193, S.194, K.195 Ligands: NA.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.20, A:V.185, A:V.185, A:K.195 Salt bridges: A:H.17, A:K.195, A:K.195 pi-Cation interactions: A:K.192, A:K.192 ADP.7: 11 residues within 4Å: Chain B: H.17, G.19, N.20, G.23, V.184, V.185, K.192, M.193, S.194, K.195 Ligands: NA.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.20, B:V.185, B:V.185, B:S.194, B:K.195 Salt bridges: B:H.17, B:K.195, B:K.195 pi-Cation interactions: B:K.192, B:K.192

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.2: 12 residues within 4Å: Chain A: L.7, G.9, Q.11, F.40, A.42, H.45, Y.127, M.131, D.134, I.135, V.143, Q.149 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.7, A:F.40, A:D.134, A:I.135, A:V.143 Hydrogen bonds: A:Q.11, A:Y.127, A:Y.127, A:Q.149, W.2 TRP.8: 10 residues within 4Å: Chain B: L.7, G.9, Q.11, F.40, H.45, M.131, D.134, I.135, V.143, Q.149 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.7, B:F.40, B:D.134, B:I.135, B:V.143 Hydrogen bonds: B:Q.149, W.8, W.8

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: L.224, G.261, Y.262, G.263, H.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.261, A:G.263, A:H.264 Salt bridges: A:H.264 PO4.4: 2 residues within 4Å: Chain A: S.206, E.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.207, A:K.208 PO4.5: 2 residues within 4Å: Chain A: R.106, Q.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.151, A:E.154 Salt bridges: A:R.106 PO4.9: 4 residues within 4Å: Chain B: S.13, G.14, K.55, N.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.14, B:N.59 Salt bridges: B:K.55

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

NA.6: 2 residues within 4Å: Chain A: S.196 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.196, A:S.196 NA.10: 3 residues within 4Å: Chain B: S.194, S.196 Ligands: ADP.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.195, B:S.196, B:S.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni complexed with ADP and Tryptophane. To be Published

Release Date

2011-10-05

Peptides

Tryptophanyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophanyl-tRNA synthetase

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