SMTL ID : 9e70.1

Human XRN1 with Adenosine-3',5'-Bisphosphate (pAp) Bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x A3P: ADENOSINE-3'-5'-DIPHOSPHATE(Non-covalent)

A3P.1: 11 residues within 4Å: Chain A: D.35, N.37, H.41, D.86, K.93, Q.97, R.100, R.101, E.178, D.208 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.35, A:Q.97 Water bridges: A:N.37, A:G.38, A:K.93, A:K.93, A:K.93, A:R.100, A:R.101, A:R.101, A:S.130, A:S.130, A:D.206, A:D.206 Salt bridges: A:K.93, A:K.93, A:R.100, A:R.101 pi-Stacking: A:H.41, A:H.41

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.86, K.93, E.176, E.178 Ligands: A3P.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.86, A:E.176, A:E.178, A3P.1, H2O.5 MG.3: 4 residues within 4Å: Chain A: K.93, E.176, E.178, D.292 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.176, A:D.292, H2O.1, H2O.5

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

EDO.4: 4 residues within 4Å: Chain A: N.95, N.291, I.294, P.295 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: P.4, D.206, A.207 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: W.9, E.12, H.304 Chain B: D.305, P.308 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: N.47, D.48, D.50, F.53, R.127 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: K.148, N.152, Y.611, T.627, Y.629 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: T.173, P.174, E.183, L.634 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 10 residues within 4Å: Chain A: T.173, E.183, C.598, I.632, S.633, L.634, D.635, A.636, W.637 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: V.354 Ligand excluded by PLIP EDO.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: E.579, T.580, C.581, N.582, H.583, S.584 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: E.623, R.624 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Y.629, K.630, I.631 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: P.123, T.124, E.125 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: S.478, W.479, Y.480, P.482 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: R.91, W.477, S.478, K.506, F.508, E.571 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain B: T.173, E.183, C.598, I.632, S.633, L.634, D.635, A.636, W.637 Ligand excluded by PLIP

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

CL.18: 3 residues within 4Å: Chain A: R.628, Y.629 Ligands: PEG.19 Ligand excluded by PLIP

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

PEG.19: 1 residues within 4Å: Ligands: CL.18 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.608

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lockbaum, G.J. et al., Characterization of exoribonuclease XRN1 as a cancer target and identification of adenosine-3',5'-bisphosphate as a potent enzyme inhibitor. Commun Biol (2025)

Release Date

2025-04-09

Peptides

5'-3' exoribonuclease 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-3' exoribonuclease 1