SMTL ID : 8uci.1

Thermophilic RNA Ligase from Palaeococcus pacificus K238G + AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: I.89, R.91, E.111, E.112, K.113, V.114, N.118, R.133, E.165, F.190, V.218, V.248, K.250 Ligands: MG.9 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.111, A:K.113, A:V.114, A:N.118, A:K.250 Water bridges: A:I.89, A:R.133 Salt bridges: A:R.91, A:K.113 pi-Stacking: A:F.190 AMP.11: 14 residues within 4Å: Chain B: I.89, R.91, E.111, E.112, K.113, V.114, N.118, R.133, E.165, F.190, V.218, V.248, K.250 Ligands: MG.17 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:E.111, B:E.111, B:K.113, B:V.114, B:N.118, B:K.250 Water bridges: B:I.89, B:I.89, B:K.113, B:R.133, B:E.245, B:E.245 Salt bridges: B:R.91, B:K.113 pi-Stacking: B:F.190

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Y.173, L.174, V.175, E.176, I.272, E.337, Y.384 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.173, A:V.175, A:E.176 Water bridges: A:E.176 GOL.3: 5 residues within 4Å: Chain A: Y.180, F.188, S.217, E.219, R.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.217, A:E.219, A:E.219, A:R.244 Water bridges: A:E.112 GOL.4: 4 residues within 4Å: Chain A: S.329, W.395, N.396 Chain B: N.97 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.329, B:N.97 Water bridges: B:Q.94, B:E.96, B:R.100 GOL.5: 6 residues within 4Å: Chain A: I.301, R.302, F.306 Chain B: E.319, V.322, E.323 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.319, B:E.323, A:I.301 Water bridges: B:E.323 GOL.6: 5 residues within 4Å: Chain A: L.207, S.217, V.218, E.219, V.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.220, A:V.220 Water bridges: A:S.217, A:S.217 GOL.7: 4 residues within 4Å: Chain A: M.58, F.77, D.78, N.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.78 GOL.8: 4 residues within 4Å: Chain A: V.175, R.275, E.337, L.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.337, A:E.337, A:L.338 Water bridges: A:R.275 GOL.12: 6 residues within 4Å: Chain B: E.112, Y.180, F.188, S.217, E.219, R.244 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.112, B:S.217, B:E.219, B:E.219, B:R.244 Water bridges: B:R.244 GOL.13: 3 residues within 4Å: Chain B: K.104, R.105, K.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.105 GOL.14: 4 residues within 4Å: Chain B: M.58, F.77, D.78, I.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.78 Water bridges: B:N.81, B:G.125 GOL.15: 6 residues within 4Å: Chain B: I.272, G.273, L.280, P.281, Y.284 Ligands: GOL.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.273 GOL.16: 8 residues within 4Å: Chain B: Y.173, L.174, V.175, I.272, I.276, E.337, Y.384 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.173, B:V.175, B:Y.384

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain A: E.165, E.245 Ligands: AMP.1 6 PLIP interactions: 5 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.1, H2O.2, H2O.3, H2O.5, AMP.1 MG.10: 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.2, H2O.3, H2O.6 MG.17: 3 residues within 4Å: Chain B: E.165, E.245 Ligands: AMP.11 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain B: D.115, E.176, A.265, 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.16, H2O.16, H2O.17

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
B

B
A

ATP dependent DNA ligase

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