SMTL ID : 8rb2.1 (1 other biounit)

The crystal structure of DNA-bound human MutSbeta (MSH2_E749A/MSH3_E976A) in the canonical mismatch bound conformation with ADP bound in MSH2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: I.648, A.649, F.650, I.651, P.670, N.671, M.672, G.673, G.674, K.675, S.676, T.677, Y.815 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:I.651, A:I.651, A:N.671, A:M.672, A:G.673, A:G.674, A:K.675, A:S.676, A:T.677, A:T.677 Water bridges: A:S.676 Salt bridges: A:K.675 pi-Stacking: A:F.650, A:Y.815, A:Y.815

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

CL.2: 2 residues within 4Å: Chain A: D.654, L.800 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: A.771 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.359 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: R.396, Q.397, A.398 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: Q.170 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: Y.465 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: N.524 Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain B: H.819 Ligand excluded by PLIP CL.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

NA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.8: 4 residues within 4Å: Chain A: A.791, I.794, P.795, V.797 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.795

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

PEG.12: 4 residues within 4Å: Chain B: Y.877, V.878, Y.1057 Ligands: GOL.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.878, B:S.904

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

EDO.13: 5 residues within 4Å: Chain B: L.330, T.331, A.332, E.512, N.514 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.331, B:N.514 EDO.17: 2 residues within 4Å: Chain B: S.323, S.324 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.324 EDO.18: 3 residues within 4Å: Chain B: H.630, K.631, K.632 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.632, B:K.632 EDO.20: 4 residues within 4Å: Chain B: K.300, G.301, Y.302, Q.449 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.301, B:Q.449 EDO.23: 2 residues within 4Å: Chain B: Y.1021, Q.1024 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.1024 EDO.24: 3 residues within 4Å: Chain B: W.562, D.565, V.869 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.562

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 8 residues within 4Å: Chain B: N.898, M.899, G.900, G.901, K.902, S.903, S.904 Ligands: PEG.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.900, B:G.901, B:K.902, B:S.903, B:S.903, B:S.904, B:S.904

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

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