SMTL ID : 8rb1.1

The crystal structure of DNA-bound human MutSbeta (MSH2_K675R/MSH3_K902R) in the canonical mismatch bound conformation with ADP bound in MSH2 and MSH3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: I.648, A.649, F.650, I.651, P.670, N.671, M.672, G.673, G.674, R.675, S.676, T.677, Y.815 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:I.651, A:I.651, A:N.653, A:N.671, A:M.672, A:G.673, A:G.674, A:R.675, A:S.676, A:T.677, A:T.677 Water bridges: A:R.675, A:S.676, A:S.676, A:S.676, A:E.749 Salt bridges: A:R.675 pi-Stacking: A:F.650, A:Y.815, A:Y.815 ADP.11: 12 residues within 4Å: Chain B: Y.661, V.662, P.681, N.682, M.683, G.684, G.685, R.686, S.687, S.688, Y.841 Ligands: MG.12 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:V.662, B:V.662, B:M.683, B:G.684, B:G.685, B:R.686, B:S.687, B:S.688, B:S.688, B:Y.841 Water bridges: B:N.664, B:R.686, B:R.686, B:S.687, B:S.687, B:S.687, B:S.687 Salt bridges: B:R.686 pi-Stacking: B:Y.661, B:Y.841, B:Y.841

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.676, D.748 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.676, H2O.2, H2O.4, H2O.5, H2O.7 MG.12: 2 residues within 4Å: Chain B: S.687 Ligands: ADP.11 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.687, H2O.13, H2O.15, H2O.16, H2O.17

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

EDO.3: 4 residues within 4Å: Chain A: S.185, K.301, C.707, S.738 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.185, A:S.738, A:S.738 Water bridges: A:D.706 EDO.4: 4 residues within 4Å: Chain A: A.771, T.772, K.773, G.775 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.771, A:K.773 EDO.5: 2 residues within 4Å: Chain A: T.788, I.865 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.788, A:T.788, A:N.792 EDO.9: 2 residues within 4Å: Chain A: S.144, Y.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.144, A:S.144 EDO.10: 3 residues within 4Å: Chain A: Y.121, Q.130, I.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.130 EDO.14: 4 residues within 4Å: Chain B: N.665, D.667, I.843, R.845 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.665, B:R.845 EDO.15: 3 residues within 4Å: Chain B: K.84, G.85, Y.86 No protein-ligand interaction detected (PLIP) EDO.16: 6 residues within 4Å: Chain B: K.24, K.28, D.29, D.46, I.49, Y.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.24, B:D.29, B:D.46 EDO.17: 3 residues within 4Å: Chain B: H.872, K.873, E.876 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain B: W.346, D.349, Q.627, V.653 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.627

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

ACT.6: 5 residues within 4Å: Chain A: R.99, K.122, S.124, N.127, F.276 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.122 Hydrogen bonds: A:S.124, A:N.127 Salt bridges: A:R.99 ACT.7: 3 residues within 4Å: Chain A: R.355, R.359, Q.601 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.359 Water bridges: A:W.345 Salt bridges: A:R.355, A:R.359 ACT.8: 2 residues within 4Å: Chain A: F.474, P.476 No protein-ligand interaction detected (PLIP) ACT.13: 3 residues within 4Å: Chain B: N.158, E.248, Y.249 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.158 Hydrogen bonds: B:Y.249

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

CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomsen, M. et al., The crystal structure of DNA-bound human MutSbeta (MSH2/MSH3) in the canonical mismatch bound conformation with ADP bound in MSH2 and MSH3. To Be Published

Release Date

2025-06-11

Peptides

DNA mismatch repair protein Msh2: A
DNA mismatch repair protein Msh3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA mismatch repair protein Msh2

DNA mismatch repair protein Msh3