SMTL ID : 6e3a.1

tRNA 2'-phosphotransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 14 residues within 4Å: Chain A: S.7, S.10, K.11, E.12, A.14, Y.15, R.18, H.19, Y.24, C.46, R.68, Y.69, R.121 Ligands: HQG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.7, A:E.12, A:R.68, A:R.68 Water bridges: A:S.10, A:R.121, A:R.121 Salt bridges: A:K.11, A:K.11, A:R.18, A:H.19, A:R.121 pi-Cation interactions: A:R.68

1 x HQG: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

HQG.2: 20 residues within 4Å: Chain A: R.18, K.66, R.68, Y.80, H.101, T.103, F.107, S.110, I.111, K.114, G.115, L.116, Q.117, Q.119, R.121, H.125, V.136, R.139, R.140 Ligands: COA.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:K.66, A:K.66, A:Y.80, A:T.103, A:G.115, A:Q.117, A:Q.119 Water bridges: A:H.101, A:R.121, A:R.140, A:R.140, A:R.140, A:R.140 Salt bridges: A:R.18, A:R.18, A:K.66, A:K.66, A:R.68, A:H.101, A:R.121, A:R.121, A:R.139, A:R.139, A:R.139, A:R.140, A:R.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banerjee, A. et al., Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4recognition and ADP-ribosylation. Nat Commun (2019)

Release Date

2019-03-20

Peptides

Probable RNA 2'-phosphotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable RNA 2'-phosphotransferase