SMTL ID : 5yzx.2 (1 other biounit)

Crystal structure of E.coli LysU T146D mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE(Non-covalent)

B4P.1: 22 residues within 4Å: Chain A: A.238, R.283, E.285, G.286, I.287, S.288, R.290, H.291, N.292, F.295, M.297, D.397, E.435, E.442, I.443, N.445, G.498, R.501, I.512 Ligands: CA.2, CA.3, CA.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.283, A:E.285, A:G.286, A:N.292, A:E.442, A:E.442, A:E.442, A:N.445, A:G.498, A:R.501 Salt bridges: A:R.283, A:R.283, A:H.291, A:R.501 pi-Stacking: A:H.291, A:F.295, A:F.295 B4P.5: 22 residues within 4Å: Chain B: A.238, R.283, E.285, G.286, I.287, S.288, R.290, H.291, N.292, F.295, M.297, D.397, E.435, E.442, I.443, N.445, G.498, R.501, I.512 Ligands: CA.6, CA.7, CA.8 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:E.285, B:G.286, B:H.291, B:N.292, B:E.442, B:E.442, B:E.442, B:N.445, B:G.498, B:R.501 Salt bridges: B:R.283, B:R.283, B:H.291, B:R.501 pi-Stacking: B:H.291, B:F.295, B:F.295

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.285 Ligands: B4P.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.285 CA.3: 4 residues within 4Å: Chain A: E.435, E.442, N.445 Ligands: B4P.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.435, A:E.442, A:E.442 CA.4: 2 residues within 4Å: Chain A: D.397 Ligands: B4P.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.397 CA.6: 2 residues within 4Å: Chain B: E.285 Ligands: B4P.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.285 CA.7: 4 residues within 4Å: Chain B: E.435, E.442, N.445 Ligands: B4P.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.435, B:E.442, B:E.442 CA.8: 2 residues within 4Å: Chain B: D.397 Ligands: B4P.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, L. et al., A proposed role for MSC to reserve the canonical function in high eukaryotes prior to stimuli. To Be Published

Release Date

2018-12-19

Peptides

Lysine--tRNA ligase, heat inducible: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Lysine--tRNA ligase, heat inducible

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