SMTL ID : 3w1g.1

Crystal Structure of Human DNA ligase IV-Artemis Complex (Native)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: E.272, T.273, K.274, L.275, D.276, E.332, F.368, E.428, M.431, K.433, W.448, K.450, K.452 Ligands: SO4.9 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.272, A:E.272, A:K.274, A:K.274, A:L.275, A:E.428, A:E.428, A:K.433, A:K.450 Water bridges: A:A.252 Salt bridges: A:K.274, A:K.274, A:K.274, A:K.450, A:K.452, A:K.452 pi-Stacking: A:F.368

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: G.277, E.278, R.279, R.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.279, A:R.279 Salt bridges: A:R.294 SO4.3: 5 residues within 4Å: Chain A: S.293, R.294, N.295, Y.297, Y.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.293, A:S.293, A:N.295, A:N.295 SO4.4: 5 residues within 4Å: Chain A: N.298, Y.299, D.301, Q.302 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.299, A:D.301, A:Q.302 SO4.5: 3 residues within 4Å: Chain A: M.81, N.298 Ligands: SO4.4 No protein-ligand interaction detected (PLIP) SO4.6: 4 residues within 4Å: Chain A: R.33, V.199, S.200, T.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.200, A:S.200 Salt bridges: A:R.33 SO4.7: 6 residues within 4Å: Chain A: H.51, V.61, T.62, D.63, R.227, H.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.61, A:R.227 Salt bridges: A:H.230 SO4.8: 2 residues within 4Å: Chain A: P.529, H.531 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.531 SO4.9: 4 residues within 4Å: Chain A: R.294, R.444, K.450 Ligands: ATP.1 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.444, A:R.444 Salt bridges: A:R.294, A:R.444, A:K.450 SO4.10: 1 residues within 4Å: Chain A: R.164 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.164 SO4.11: 4 residues within 4Å: Chain A: F.530, H.531, R.532, K.533 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.532, A:K.533 Salt bridges: A:H.531 SO4.12: 2 residues within 4Å: Chain A: R.532, K.545 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.545, A:K.545 Salt bridges: A:K.545 SO4.13: 6 residues within 4Å: Chain A: L.215, T.219, Q.228, L.236, S.240, T.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.240 SO4.14: 4 residues within 4Å: Chain A: K.163, R.164, K.165, D.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.165, A:D.166 SO4.15: 3 residues within 4Å: Chain A: E.278, Q.302, T.363 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.302 SO4.16: 8 residues within 4Å: Chain A: T.342, K.474, G.475, S.476, M.480, M.481, G.510, C.511 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.342, A:K.474, A:S.476, A:C.511

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ochi, T. et al., Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds light on double-strand break repair. Structure (2013)

Release Date

2013-04-03

Peptides

DNA ligase 4: A
Artemis-derived peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA ligase 4

Artemis-derived peptide

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