SMTL ID : 7rpw.1

Archaeal DNA ligase and heterotrimeric PCNA in complex with adenylated DNA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 6 residues within 4Å: Chain D: G.20, C.21 Chain G: L.79, G.80, I.81, G.82 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:G.80, G:I.81 MN.2: 2 residues within 4Å: Chain D: G.20, C.21 No protein-ligand interaction detected (PLIP) MN.4: 3 residues within 4Å: Chain D: G.22 Chain G: D.72, E.78 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.72 MN.5: 6 residues within 4Å: Chain G: K.280, Y.281, D.282, E.330, E.429 Ligands: AMP.3 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:Y.281, G:E.429

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 14 residues within 4Å: Chain E: G.1 Chain G: Y.279, K.280, Y.281, D.282, G.283, R.285, R.300, E.330, E.429, M.432, K.434, W.451 Ligands: MN.5 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:Y.279, G:Y.281, G:R.285, G:R.300, G:R.300, G:E.429, G:E.429, G:K.434 Salt bridges: G:K.280, G:K.453

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sverzhinsky, A. et al., Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure (2022)

Release Date

2021-11-17

Peptides

DNA polymerase sliding clamp 1: A
DNA polymerase sliding clamp 2: B
DNA polymerase sliding clamp 3: C
DNA ligase: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

G
E

DNA polymerase sliding clamp 1

DNA polymerase sliding clamp 2

DNA polymerase sliding clamp 3

DNA ligase

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