SMTL ID : 5d1o.1

Archaeal ATP-dependent RNA ligase - form 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: F.68, K.70, I.71, R.73, E.92, E.93, K.94, M.95, N.99, R.115, E.148, F.172, V.200, E.228, V.231, K.233, K.243 Ligands: SO4.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:I.71, A:I.71, A:R.73, A:E.92, A:K.94, A:M.95, A:N.99, A:K.233 Water bridges: A:R.115, A:R.115 Salt bridges: A:K.94, A:R.115, A:K.243, A:K.243, A:K.243 pi-Stacking: A:F.172

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.73, K.243, R.275 Chain B: Y.378 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.73, A:K.243, A:R.275 SO4.3: 2 residues within 4Å: Chain A: P.17, R.20 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.20 SO4.4: 5 residues within 4Å: Chain B: R.73, K.94, K.243, R.275 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.275 Salt bridges: B:R.73, B:K.243 SO4.5: 6 residues within 4Å: Chain B: K.70, I.71, K.94, R.115, K.243 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.71, B:I.71 Salt bridges: B:K.70, B:R.115, B:K.243 SO4.6: 3 residues within 4Å: Chain B: Q.159, D.160, R.252 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.160 Salt bridges: B:R.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain B: K.94, M.95, E.148, E.228 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.94, B:E.148, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, H. et al., Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis. Nucleic Acids Res. (2016)

Release Date

2016-03-09

Peptides

ATP-dependent RNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent RNA ligase

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