SMTL ID : 8tfx.1

tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with 2',5'-ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x A2P: ADENOSINE-2'-5'-DIPHOSPHATE(Non-covalent)

A2P.1: 12 residues within 4Å: Chain A: F.3, S.6, K.7, A.10, R.14, K.60, R.62, Y.63, Y.74, R.133 Ligands: EDO.3, GOL.7 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.6, A:S.6, A:K.7, A:R.14, A:Y.74, A:Y.74, A:Y.74 Water bridges: A:H.15, A:K.60, A:R.133, A:R.133, A:R.133, A:R.133, A:R.133 Salt bridges: A:R.14, A:K.60, A:R.62, A:R.133, A:R.133 pi-Cation interactions: A:R.62

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: H.95, G.96, T.97, N.101, M.113, H.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.101 EDO.3: 6 residues within 4Å: Chain A: K.7, A.10, Y.11, H.15 Ligands: A2P.1, GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.7, A:H.15 EDO.4: 4 residues within 4Å: Chain A: E.19, F.20, K.41 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.19, A:E.19 EDO.5: 5 residues within 4Å: Chain A: L.8, Y.11, E.19, F.20 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: W.18, P.24, D.25, E.26, Y.78, P.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.25 EDO.8: 7 residues within 4Å: Chain A: Y.74, G.75, H.76, L.82, R.115, Y.117, H.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.75, A:H.76, A:H.76, A:H.119

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: K.7 Ligands: A2P.1, EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.7

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain A: V.98, R.99, R.100, D.137 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: S.121, T.130 Ligands: K.13 Ligand excluded by PLIP

6 x K: POTASSIUM ION(Non-covalent)

K.11: 6 residues within 4Å: Chain A: L.13, G.28, R.71, A.72, H.76, Y.78 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.13, A:G.28 K.12: 5 residues within 4Å: Chain A: E.86, D.87, R.149, K.154, I.155 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.86 K.13: 7 residues within 4Å: Chain A: Y.94, H.95, G.96, H.119, A.127, T.130 Ligands: CL.10 No protein-ligand interaction detected (PLIP) K.14: 3 residues within 4Å: Chain A: T.47, E.48, E.49 No protein-ligand interaction detected (PLIP) K.15: 4 residues within 4Å: Chain A: E.23, V.30, S.31, E.34 No protein-ligand interaction detected (PLIP) K.16: 3 residues within 4Å: Chain A: S.6, I.54, D.58 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.6, A:D.58, H2O.2, H2O.3

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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