SMTL ID : 3w5o.1 (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: 16 residues within 4Å: Chain A: E.272, T.273, K.274, L.275, D.276, G.277, R.279, E.332, F.368, E.428, M.431, K.433, W.448, K.450, K.452 Ligands: SO4.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.272, A:L.275, A:L.275, A:G.277, A:R.279, A:R.294, A:K.433, A:K.450, A:K.450 Water bridges: A:R.444 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

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

SO4.2: 3 residues within 4Å: Chain A: I.416, N.420, R.578 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.420 Salt bridges: A:R.578 SO4.3: 2 residues within 4Å: Chain A: P.529, H.531 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.531 SO4.4: 5 residues within 4Å: Chain A: G.277, E.278, R.279, R.294 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.279, A:E.332 Salt bridges: A:R.294 SO4.5: 4 residues within 4Å: Chain A: S.293, N.295, Y.297, Y.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.293, A:N.295, A:N.295, A:Y.299 SO4.6: 5 residues within 4Å: Chain A: N.298, Y.299, T.300, D.301, Q.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.298, A:Q.302 SO4.7: 1 residues within 4Å: Chain A: R.33 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.33 SO4.8: 3 residues within 4Å: Chain A: T.382, R.384, K.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.382 SO4.9: 8 residues within 4Å: Chain A: T.342, G.475, S.476, M.480, M.481, S.509, G.510, C.511 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.340, A:S.509, A:C.511 SO4.10: 1 residues within 4Å: Chain A: K.545 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.545 SO4.11: 5 residues within 4Å: Chain A: R.33, G.198, V.199, S.200, T.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.200, A:T.203 Salt bridges: A:R.33 SO4.12: 2 residues within 4Å: Chain A: W.591, H.592 No protein-ligand interaction detected (PLIP) SO4.13: 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 SO4.14: 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

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
A

DNA ligase 4

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