SMTL ID : 6ras.1

Pmar-Lig_Pre.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 7 residues within 4Å: Chain B: C.9, C.10 Chain C: C.1 Chain D: K.126, L.147, R.187, R.334 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.187, D:R.334 PGE.3: 10 residues within 4Å: Chain D: F.143, I.176, R.178, K.181, V.182, E.183, F.185, L.254, F.257, Q.258 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.176, D:E.183

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 17 residues within 4Å: Chain C: C.1, A.2 Chain D: L.147, A.148, E.165, I.166, K.167, L.168, R.172, E.220, F.249, L.290, M.322, K.324, R.334, W.338, K.340 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.165, D:E.165, D:K.167, D:L.168, D:R.172, D:K.324, D:R.334 Salt bridges: D:K.167, D:K.340 pi-Stacking: D:F.249

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

SO4.4: 3 residues within 4Å: Chain D: K.274, E.291, W.292 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.291, D:W.292 Salt bridges: D:K.274 SO4.5: 4 residues within 4Å: Chain D: H.149, D.150, N.153, H.154 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.150, D:N.153 Salt bridges: D:H.149, D:H.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williamson, A. et al., Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation. Nucleic Acids Res. (2019)

Release Date

2019-07-10

Peptides

ATP-dependent DNA ligase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
I

ATP-dependent DNA ligase