SMTL ID : 6rau.1

PostS3_Pmar_lig4_WT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 18 residues within 4Å: Chain B: C.11 Chain C: L.147, A.148, E.165, I.166, K.167, L.168, V.171, R.172, R.187, E.220, F.249, L.290, M.322, K.324, R.334, W.338, K.340 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.165, C:E.165, C:K.167, C:L.168, C:R.172, C:K.324, C:R.334 Water bridges: C:R.172 Salt bridges: C:K.167, C:K.340 pi-Stacking: C:F.249

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

SO4.2: 2 residues within 4Å: Chain C: R.178, Q.179 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.179 Salt bridges: C:R.178 SO4.3: 3 residues within 4Å: Chain C: K.274, E.291, W.292 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.291 Water bridges: C:K.274, C:K.274 Salt bridges: C:K.274 SO4.4: 5 residues within 4Å: Chain C: H.149, D.150, N.153, H.154, R.334 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.150, C:D.150, C:N.153 Salt bridges: C:H.149, C: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: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
I

ATP-dependent DNA ligase