SMTL ID : 9c6m.2 (1 other biounit)

Yasminevirus c12orf29, a 5' to 3' RNA ligase, K73M mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.1: 17 residues within 4Å: Chain A: V.21, K.24, I.25, T.72, A.73, M.74, T.75, C.79, R.90, E.175, H.196, G.197, V.244, H.246, M.252, K.254, H.259 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:I.25, A:T.72, A:T.75, A:T.75, A:R.90, A:E.175, A:H.196, A:G.197, A:H.246 Water bridges: A:T.198 Salt bridges: A:K.24, A:K.24, A:K.24, A:R.90, A:K.254, A:K.254, A:K.254 pi-Stacking: A:H.196, A:H.196 ATP.2: 17 residues within 4Å: Chain B: V.21, K.24, I.25, Y.49, T.72, A.73, M.74, T.75, C.79, R.90, E.175, H.196, G.197, V.244, H.246, M.252, K.254 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:I.25, B:T.72, B:T.75, B:T.75, B:E.175, B:H.196, B:G.197, B:H.246 Salt bridges: B:R.90, B:K.254, B:K.254, B:K.254 pi-Cation interactions: B:H.196, B:H.196 ATP.3: 16 residues within 4Å: Chain C: V.21, K.24, I.25, T.72, A.73, M.74, T.75, C.79, R.90, E.175, H.196, G.197, V.244, H.246, M.252, K.254 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:I.25, C:A.73, C:T.75, C:E.175, C:G.197, C:H.246 Salt bridges: C:K.24, C:K.24, C:K.24, C:R.90, C:K.254, C:K.254, C:K.254 pi-Stacking: C:H.196, C:H.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Y. et al., Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation. To Be Published

Release Date

2024-10-02

Peptides

RNA ligase1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

RNA ligase1

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