SMTL ID : 7lw9.1

Human Exonuclease 5 crystal structure in complex with ssDNA, Sm, and Na

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

monomer

Ligands

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

SF4.1: 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

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: D.155, L.170, T.172 Chain B: G.10 Ligands: SM.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.172 Water bridges: A:L.170, A:T.172 ACT.3: 2 residues within 4Å: Chain A: D.243, E.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.243 ACT.9: 6 residues within 4Å: Chain A: L.51, Y.53, Y.55, D.58, K.73 Chain B: T.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.55 Salt bridges: A:K.73

2 x SM: SAMARIUM (III) ION(Non-covalent)

SM.4: 6 residues within 4Å: Chain A: D.155, E.169, L.170 Chain B: A.9, G.10 Ligands: ACT.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.155, A:E.169, A:L.170, H2O.1, ACT.2 SM.5: 1 residues within 4Å: Chain A: E.138 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: E.138, D.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.138

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

EDO.7: 3 residues within 4Å: Chain A: H.50, L.51, K.52 No protein-ligand interaction detected (PLIP) EDO.8: 7 residues within 4Å: Chain A: V.308, D.309, V.310, A.313, C.316, W.327, R.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.308

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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