SMTL ID : 3w5o.2 (1 other biounit)

Crystal Structure of Human DNA ligase IV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

monomer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: E.272, T.273, K.274, L.275, D.276, R.279, E.332, K.346, F.368, E.428, M.431, K.433, W.448, K.450, K.452 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.272, A:E.272, A:L.275, A:L.275, A:R.279, A:K.433, A:R.444, A:K.450, A:K.450 Water bridges: A:R.444 Salt bridges: A:K.274, A:K.274, A:K.274, A:K.346, A:K.450, A:K.452, A:K.452

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

SO4.2: 2 residues within 4Å: Chain A: P.529, H.531 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.531 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: 4 residues within 4Å: Chain A: N.298, Y.299, D.301, Q.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.302 SO4.5: 1 residues within 4Å: Chain A: R.164 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.164 SO4.6: 1 residues within 4Å: Chain A: D.166 No protein-ligand interaction detected (PLIP) SO4.7: 3 residues within 4Å: Chain A: Q.75, S.200, Q.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.75, A:Q.201, A:Q.201 SO4.8: 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 SO4.9: 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 SO4.10: 5 residues within 4Å: Chain A: G.277, E.278, R.279, R.294, K.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.279, A:R.279 Salt bridges: A:K.346 SO4.11: 2 residues within 4Å: Chain A: R.227, Q.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.228 Salt bridges: A:R.227 SO4.12: 1 residues within 4Å: Chain A: S.537 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.537

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA ligase 4

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