SMTL ID : 5dac.1

ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

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

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

AGS.2: 27 residues within 4Å: Chain A: R.13, S.14, Y.35, 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: D.298, M.328, M.335, R.340, S.342, A.343, G.344, Q.345 Ligands: MG.1 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.13, A:S.14, A:N.36, A:G.37, A:G.37, A:S.38, A:G.39, A:K.40, A:T.41, A:T.42, A:A.64, A:D.68, A:R.431, B:D.298, B:S.342, B:A.343, B:G.344, B:Q.345, B:Q.345 Water bridges: A:T.41, A:T.41, A:D.371, A:R.431 Salt bridges: A:K.40 AGS.5: 27 residues within 4Å: Chain A: D.298, M.328, R.340, S.342, A.343, G.344, Q.345 Chain B: R.13, S.14, Y.35, N.36, G.37, S.38, G.39, K.40, T.41, T.42, G.63, A.64, I.66, H.67, D.68, L.71, Q.159, H.409, R.431 Ligands: MG.4 22 PLIP interactions: 16 interactions with chain B, 6 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:T.42, B:A.64, B:D.68, B:Q.159, B:R.431, A:D.298, A:S.342, A:A.343, A:G.344, A:Q.345, A:Q.345 Salt bridges: B:K.40

2 x AES: 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE(Non-covalent)

AES.3: 9 residues within 4Å: Chain A: T.285, E.288, L.289, L.355, A.358, E.359, G.366, I.392, R.396 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.285, A:I.392 Hydrogen bonds: A:R.396 AES.6: 10 residues within 4Å: Chain B: T.285, E.288, L.289, L.355, A.358, E.359, I.368, I.392, R.396, L.402 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.359, B:E.359

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative uncharacterized protein,Putative uncharacterized protein