SMTL ID : 6imj.1

The crystal structure of Se-AsfvLIG:DNA complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 15 residues within 4Å: Chain A: L.128, V.129, Q.149, R.150, K.151, R.152, R.156, R.172, E.203, F.232, I.294, R.296, K.316 Ligands: CD.3, CD.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.129, A:Q.149, A:K.151, A:R.152, A:R.156, A:R.296 Salt bridges: A:K.151, A:R.172, A:R.172, A:K.316, A:K.316, A:K.316, A:K.318 pi-Stacking: A:F.232 ATP.6: 15 residues within 4Å: Chain B: L.128, V.129, Q.149, R.150, K.151, R.152, R.156, R.172, E.203, F.232, I.294, R.296, K.316 Ligands: CD.8, CD.9 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:V.129, B:Q.149, B:R.150, B:K.151, B:R.152, B:R.156, B:E.291, B:R.296 Water bridges: B:K.316, B:K.316 Salt bridges: B:K.151, B:R.172, B:R.172, B:K.316, B:K.316, B:K.316, B:K.318 pi-Stacking: B:F.232

6 x CD: CADMIUM ION(Non-covalent)

CD.2: 4 residues within 4Å: Chain A: L.377, K.380, H.381, I.419 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.419 CD.3: 3 residues within 4Å: Chain A: R.172, H.310 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) CD.4: 6 residues within 4Å: Chain A: K.151, R.152, N.153, E.203, E.291 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) CD.7: 3 residues within 4Å: Chain B: L.377, H.381, I.419 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.381, B:I.419 CD.8: 2 residues within 4Å: Chain B: H.310 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) CD.9: 2 residues within 4Å: Chain B: G.154 Ligands: ATP.6 No protein-ligand interaction detected (PLIP)

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

CL.5: 4 residues within 4Å: Chain A: R.150, R.152, V.267, E.268 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues. Nat Commun (2019)

Release Date

2019-02-27

Peptides

DNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA ligase

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