SMTL ID : 7auc.1

Crystal structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

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

ACT.1: 4 residues within 4Å: Chain A: N.224, P.225, Y.434, F.435 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.225 Water bridges: A:R.226, A:Y.434 ACT.2: 8 residues within 4Å: Chain A: P.80, T.81, G.82, G.83, M.245, N.248, R.249, H.250 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.80 Hydrogen bonds: A:H.250 Salt bridges: A:R.249, A:H.250 ACT.4: 4 residues within 4Å: Chain A: F.76, Q.228, K.229, L.232 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.76, A:L.232 ACT.10: 4 residues within 4Å: Chain A: K.358, I.395, E.398, H.409 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.358, A:H.409

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

EDO.3: 6 residues within 4Å: Chain A: A.223, Q.228, F.247, F.435, G.436, E.437 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.435, A:E.437 EDO.6: 3 residues within 4Å: Chain A: K.47, K.51, K.52 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.52 EDO.7: 4 residues within 4Å: Chain A: M.46, K.47, H.50, K.51 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: N.506, V.508, T.509, D.528, G.529 Ligands: ADP.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.506, A:D.528 Water bridges: A:R.59, A:K.512, A:D.528 EDO.9: 8 residues within 4Å: Chain A: D.112, Q.113, K.116, P.346, R.372, F.502, N.503 Ligands: ADP.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.112, A:Q.113, A:R.372, A:R.372 EDO.12: 2 residues within 4Å: Chain A: Y.385, Y.414 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 6 residues within 4Å: Chain A: H.250, N.251, G.374, F.444, H.448, V.451 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.374 PG4.13: 5 residues within 4Å: Chain A: L.37, M.46, H.56, N.57, F.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.58 Water bridges: A:N.57, A:F.58

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 9 residues within 4Å: Chain A: Y.284, C.285, L.286, I.337, H.353, S.355, L.356, P.357, E.366 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.355, A:S.355, A:E.366 Water bridges: A:K.358, A:K.358

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

ADP.14: 19 residues within 4Å: Chain A: L.55, N.57, F.58, R.59, Q.62, P.80, T.81, G.82, G.83, G.84, K.85, S.86, R.372, N.506, D.528 Ligands: EDO.8, EDO.9, MG.15, CA.18 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:N.57, A:R.59, A:R.59, A:R.59, A:Q.62, A:P.80, A:G.82, A:G.83, A:G.84, A:K.85, A:S.86, A:S.86, A:S.86, A:N.506 Water bridges: A:T.81, A:K.85, A:L.87, A:Q.113, A:Q.113, A:E.186, A:E.186, A:R.372 Salt bridges: A:K.85, A:R.372 pi-Cation interactions: A:R.59, A:R.59

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.15: 1 residues within 4Å: Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain A: D.74, L.238 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.74, A:L.238, H2O.5, H2O.7, H2O.12

1 x ZN: ZINC ION(Non-covalent)

ZN.17: 4 residues within 4Å: Chain A: C.426, C.445, C.453, C.456 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.426, A:C.445, A:C.453, A:C.456

2 x CA: CALCIUM ION(Non-covalent)

CA.18: 2 residues within 4Å: Chain A: K.116 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) CA.19: 2 residues within 4Å: Chain A: E.437, F.440 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein. Elife (2021)

Release Date

2020-12-16

Peptides

Bloom syndrome protein,Bloom syndrome protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bloom syndrome protein,Bloom syndrome protein