SMTL ID : 8eza.1

NHEJ Long-range complex with PAXX

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-4-2-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain E: M.3729, S.3731, L.3732, R.3733, P.3735, L.3751, K.3753, E.3756, E.3804, W.3805, L.3806, M.3929, I.3940, D.3941 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.3731, E:S.3731, E:R.3733, E:E.3804, E:L.3806, E:D.3941, E:D.3941 Salt bridges: E:K.3753, E:K.3753 ATP.2: 13 residues within 4Å: Chain L: M.3729, S.3731, L.3732, R.3733, P.3735, L.3751, K.3753, E.3756, E.3804, W.3805, M.3929, I.3940, D.3941 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:S.3731, L:S.3731, L:R.3733, L:E.3804, L:D.3941 Salt bridges: L:K.3753, L:K.3753

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ. Sci Adv (2023)

Release Date

2023-06-14

Peptides

Protein PAXX: AS
X-ray repair cross-complementing protein 6: BC
X-ray repair cross-complementing protein 5: DK
DNA-dependent protein kinase catalytic subunit: EL
PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit -- Unknown region: FM
Non-homologous end-joining factor 1: IJ
DNA repair protein XRCC4: PRTV
DNA ligase 4: QU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

S
T

B
J

C
A

D
K

K
B

E
L

L
C

F
R

M
Q

I
H

J
I

P
F

R
G

T
O

V
P

Q
X

U
Y

Protein PAXX

X-ray repair cross-complementing protein 6

X-ray repair cross-complementing protein 5

DNA-dependent protein kinase catalytic subunit

PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit -- Unknown region

Non-homologous end-joining factor 1

DNA repair protein XRCC4

DNA ligase 4

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