SMTL ID : 8ucf.1

Thermophilic RNA Ligase from Palaeococcus pacificus K238G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: V.175, I.272, G.273, Y.284, E.337, Y.384 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.337 Water bridges: A:V.175, A:G.273, A:G.273 GOL.2: 4 residues within 4Å: Chain A: R.91, V.261, R.291 Chain B: D.402 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:V.401, A:V.92, A:V.261, A:R.291, A:R.291, A:R.291 GOL.3: 5 residues within 4Å: Chain A: M.58, F.77, D.78, N.81, G.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.78, A:D.78, A:N.81 Water bridges: A:G.57 GOL.4: 6 residues within 4Å: Chain A: I.89, E.111, K.113, F.190, V.248, K.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.111, A:K.250 Water bridges: A:K.113 GOL.5: 7 residues within 4Å: Chain A: F.278, E.390, L.394, F.400 Chain B: Q.287, K.290 Ligands: GOL.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.287, A:E.390 GOL.6: 7 residues within 4Å: Chain A: M.286, Q.287, K.290 Chain B: F.277, F.278, E.390 Ligands: GOL.13 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.287, A:K.290, B:F.277 Water bridges: B:D.279 GOL.9: 6 residues within 4Å: Chain B: V.175, I.272, G.273, Y.284, E.337, Y.384 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.337 Water bridges: B:V.175, B:G.273, B:G.273 GOL.10: 4 residues within 4Å: Chain A: D.402 Chain B: R.91, V.261, R.291 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Water bridges: B:V.92, B:V.261, B:R.291, B:R.291, B:R.291, A:V.401 GOL.11: 5 residues within 4Å: Chain B: M.58, F.77, D.78, N.81, G.125 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.78, B:N.81 Water bridges: B:G.57 GOL.12: 6 residues within 4Å: Chain B: I.89, E.111, K.113, F.190, V.248, K.250 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.250 Water bridges: B:K.113 GOL.13: 7 residues within 4Å: Chain A: Q.287, K.290 Chain B: F.278, E.390, L.394, F.400 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.287 GOL.14: 7 residues within 4Å: Chain A: F.277, F.278, E.390 Chain B: M.286, Q.287, K.290 Ligands: GOL.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.287, B:K.290, A:F.277 Water bridges: A:D.279

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: D.115, E.176, D.269 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.115, A:E.176, A:D.269, H2O.1, H2O.3, H2O.3 MG.8: 3 residues within 4Å: Chain A: K.113, G.116, E.165 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain B: D.115, E.176, D.269 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.115, B:E.176, B:D.269, H2O.10, H2O.11, H2O.11 MG.16: 3 residues within 4Å: Chain B: K.113, G.116, E.165 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rousseau, M. et al., Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus. Nucleic Acids Res. (2024)

Release Date

2024-02-21

Peptides

ATP dependent DNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ATP dependent DNA ligase

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