SMTL ID : 8tg3.1

tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-1" -phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

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.1: 16 residues within 4Å: Chain A: R.34, R.83, Y.95, H.116, T.118, A.122, L.125, I.126, G.130, I.131, M.132, R.136, T.151, R.154, H.155 Ligands: GOL.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.118, A:G.130, A:M.132 Water bridges: A:R.83, A:H.116, A:G.117, A:R.136, A:T.151, A:H.155, A:H.155 Salt bridges: A:R.34, A:R.34, A:R.83, A:H.116, A:R.136, A:R.136, A:R.136, A:R.154, A:R.154, A:R.154, A:H.155, A:H.155

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 4 residues within 4Å: Chain A: P.110, R.170, K.175, V.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.170, A:R.170, A:V.176 NO3.5: 3 residues within 4Å: Chain A: M.21, R.22, V.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.22, A:R.22, A:V.23 Water bridges: A:R.22 NO3.6: 4 residues within 4Å: Chain A: H.36, P.37, G.38, R.39 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.36, A:G.38, A:R.39, A:R.39

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: T.119, E.120, E.121, G.156, N.157, L.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.120, A:E.121, A:N.157, A:L.158 GOL.4: 8 residues within 4Å: Chain A: K.27, A.30, G.31, R.34, H.35, R.136, R.154 Ligands: HQG.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.27, A:R.34, A:H.35, A:R.136, A:R.136, A:R.154

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: P.80, K.81, S.144, D.147, T.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.182

1 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain A: P.105, L.106, G.108, E.177, R.178 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacewicz, A. et al., Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-11-08

Peptides

Probable RNA 2'-phosphotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable RNA 2'-phosphotransferase

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