SMTL ID : 7sgl.1

DNA-PK complex of DNA end processing

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: H.3924, N.3927, D.3941 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.3941 MG.4: 7 residues within 4Å: Chain D: H.33, H.35, D.37, H.38, D.136 Chain E: A.25 Ligands: MG.5 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.37, D:D.37, D:H.38, D:D.136 MG.5: 7 residues within 4Å: Chain D: H.33, H.35, H.115, D.136, H.319 Chain E: A.25 Ligands: MG.4 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.33, D:H.35, D:H.115, D:D.136

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 16 residues within 4Å: Chain A: M.3729, S.3731, L.3751, K.3753, I.3803, E.3804, W.3805, L.3806, T.3811, H.3924, N.3926, M.3929, I.3940, D.3941, K.4023 Ligands: MG.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.3804, A:L.3806, A:N.3926, A:N.3926 Salt bridges: A:K.3753, A:H.3924, A:K.4023, A:K.4023 pi-Stacking: A:W.3805

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.3: 10 residues within 4Å: Chain B: K.360, H.362, H.363, K.446 Chain C: K.363, H.411, K.413, H.414, Y.416, K.481 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:Y.416, C:Y.416 Salt bridges: C:K.363, C:K.413, C:H.414, C:K.481, C:K.481, B:K.360, B:K.360, B:K.360, B:H.362, B:H.363, B:K.446

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain D: H.228, H.254, C.256, C.272 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.228, D:H.254, D:C.256, D:C.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Autophosphorylation transforms DNA-PK from protecting to processing DNA ends. Mol.Cell (2022)

Release Date

2022-01-12

Peptides

DNA-dependent protein kinase catalytic subunit: A
X-ray repair cross-complementing protein 6: B
X-ray repair cross-complementing protein 5: C
Protein artemis: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DNA-dependent protein kinase catalytic subunit

X-ray repair cross-complementing protein 6

X-ray repair cross-complementing protein 5

Protein artemis

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