SMTL ID : 7zr1.1

Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite structure)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-mer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: D.17, H.19, D.57, H.213, H.241, H.243 Ligands: MN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.17, A:H.19, A:D.57, A:H.243 MN.2: 6 residues within 4Å: Chain A: D.17, D.57, N.124, H.213, H.241 Ligands: MN.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.57, A:H.213, A:H.241 MN.3: 6 residues within 4Å: Chain B: D.17, H.19, D.57, H.241, H.243 Ligands: MN.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.17, B:H.19, B:H.243 MN.4: 6 residues within 4Å: Chain B: D.17, D.57, H.213, H.216, H.241 Ligands: MN.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.57, B:H.213, B:H.216, B:H.241

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain C: T.41, Q.159, E.1238 Chain D: G.1205 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.41 MG.7: 4 residues within 4Å: Chain D: T.41, Q.159, D.1237 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.41

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.6: 21 residues within 4Å: Chain C: R.13, S.14, N.36, G.37, S.38, G.39, K.40, T.41, T.42, A.64, I.66, D.68, L.71, Q.159, E.1238, H.1275 Chain D: M.1201, G.1205, R.1206, C.1207 Ligands: MG.5 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.13, C:S.14, C:G.37, C:S.38, C:G.39, C:K.40, C:K.40, C:T.41, C:T.41, C:T.42, C:T.42, C:A.64, C:D.68, C:Q.159, C:R.1297, D:C.1207 Salt bridges: C:K.40, D:R.1206 AGS.8: 12 residues within 4Å: Chain C: R.1206 Chain D: R.13, Y.35, N.36, G.37, S.38, G.39, K.40, T.41, T.42, Q.159 Ligands: MG.7 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.37, D:G.37, D:S.38, D:G.39, D:K.40, D:T.41, D:T.41, D:T.42, D:T.42, D:Q.159, C:R.1206 Salt bridges: D:K.40 pi-Cation interactions: D:R.13, D:R.13, C:R.1206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rotheneder, M. et al., Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions. Mol.Cell (2023)

Release Date

2023-01-11

Peptides

Double-strand break repair protein: AB
DH domain-containing protein: CD
FHA domain-containing protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Double-strand break repair protein

DH domain-containing protein

FHA domain-containing protein