SMTL ID : 5da9.1

ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with the Rad50-binding domain of Mre11

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-oligomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.41, Q.159, D.371 Ligands: AGS.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.41, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: A.343 Chain B: T.41, Q.159, D.371 Ligands: AGS.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.41, H2O.1, H2O.1

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

AGS.2: 24 residues within 4Å: Chain A: R.13, S.14, N.36, G.37, S.38, G.39, K.40, T.41, T.42, A.64, I.66, H.67, D.68, L.71, Q.159, H.409, R.431 Chain B: M.328, R.340, S.342, A.343, G.344, Q.345 Ligands: MG.1 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.13, A:N.36, A:G.37, A:G.37, A:G.39, A:K.40, A:T.41, A:T.41, A:T.42, A:T.42, A:A.64, A:D.68, A:Q.159, A:R.431, B:S.342, B:A.343, B:G.344, B:Q.345, B:Q.345 Water bridges: A:T.41, B:S.342 Salt bridges: A:K.40 AGS.4: 23 residues within 4Å: Chain A: D.298, M.335, R.340, S.342, A.343, G.344, Q.345 Chain B: R.13, S.14, N.36, G.37, S.38, G.39, K.40, T.41, T.42, A.64, I.66, H.67, D.68, Q.159, H.409 Ligands: MG.3 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.13, B:S.14, B:N.36, B:G.37, B:G.37, B:S.38, B:G.39, B:K.40, B:T.41, B:T.42, B:A.64, B:D.68, A:S.342, A:A.343, A:G.344, A:Q.345 Water bridges: B:Q.159, B:Q.159 Salt bridges: B:K.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seifert, F.U. et al., Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50. Embo J. (2016)

Release Date

2016-03-02

Peptides

Putative uncharacterized protein,Putative uncharacterized protein: AB
Putative double-strand break protein: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative uncharacterized protein,Putative uncharacterized protein

Putative double-strand break protein