SMTL ID : 6bkf.1

Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG- DA- DC: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')(Non-covalent)

DG-DT-DC-DG-DG-DA-DC.1: 15 residues within 4Å: Chain A: I.254, R.294, R.444, K.450, K.452 Chain B: C.11 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7, G.8 Ligands: AMP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.200

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.2: 14 residues within 4Å: Chain A: E.272, T.273, K.274, L.275, R.279, E.332, F.368, E.428, M.431, K.433, W.448, K.450, K.452 Ligands: DG-DT-DC-DG-DG-DA-DC.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.272, A:L.275, A:R.279, A:K.433 Salt bridges: A:K.274, A:K.450, A:K.452 pi-Stacking: A:F.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaminski, A.M. et al., Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis. Nat Commun (2018)

Release Date

2018-07-18

Peptides

DNA ligase 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase 4

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