SMTL ID : 7lw7.1

Human Exonuclease 5 crystal structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: K.185, C.188, F.189, S.192, V.288, K.291 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.185, A:S.192, A:S.192, A:K.291, A:K.291

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 11 residues within 4Å: Chain A: C.65, L.67, Q.68, Y.71, G.307, V.308, C.316, C.319, A.322, C.325, W.327 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.65, A:C.316, A:C.319, A:C.325

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

EDO.3: 8 residues within 4Å: Chain A: Y.55, V.56, T.57, R.97, L.101, G.152, V.153, Y.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.56, A:T.57, A:V.153, A:Y.194, A:Y.194 EDO.4: 7 residues within 4Å: Chain A: N.63, W.64, C.65, V.308, D.309, E.312, K.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.64, A:D.309, A:D.309 Water bridges: A:E.66 EDO.5: 9 residues within 4Å: Chain A: F.120, F.142, V.206, T.207, P.208, L.211, M.245, V.248, F.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.206 EDO.6: 4 residues within 4Å: Chain A: F.49, Y.71, E.74, P.305 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.48, A:Y.298 EDO.7: 6 residues within 4Å: Chain A: Q.68, L.79, T.318, C.319, T.320, Y.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.318, A:T.320, A:T.320 EDO.8: 2 residues within 4Å: Chain A: V.109, T.110 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hambarde, S. et al., EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart. Mol.Cell (2021)

Release Date

2021-07-14

Peptides

Exonuclease V: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Exonuclease V

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