SMTL ID : 6bkg.1

Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

DG-DT-DC-DG-DG-DA-DC.1: 23 residues within 4Å: Chain A: K.274, R.294, K.450, K.452, Y.455, G.510, C.511, T.512, M.513, F.579, R.581, E.583 Chain B: C.11 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7, G.8 Ligands: NA.4, AMP.6 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:Q.75, A:Q.75, A:D.194, A:Q.201, A:Q.202, A:K.346, A:K.474, A:S.482, A:S.482, A:R.506, A:Y.571 Water bridges: A:D.194, A:K.196, A:S.476, A:S.476, A:R.477, A:R.477 Salt bridges: A:K.196, A:R.477, A:H.483, A:H.483, A:R.506

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: S.206, V.207, N.210 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: Y.299, D.301, Q.302 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: G.510, I.582 Ligands: DG-DT-DC-DG-DG-DA-DC.1, DG-DT-DC-DG-DG-DA-DC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.582

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: E.515, D.518, L.519, I.585, D.587 No protein-ligand interaction detected (PLIP)

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 15 residues within 4Å: Chain A: E.272, T.273, K.274, L.275, R.279, R.294, E.332, F.368, M.431, K.433, R.444, W.448, K.450, K.452 Ligands: DG-DT-DC-DG-DG-DA-DC.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.272, A:E.272, A:K.274, A:L.275, A:R.279, A:R.294, A:K.433, A:R.444 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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