SMTL ID : 8iqi.1

Structure of Full-Length AsfvPrimPol in Complex-Form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 18 residues within 4Å: Chain A: A.602, G.640, C.641, N.642, G.643, K.644, T.645, F.646, F.764, E.778, D.779, P.780, F.782 Chain B: N.712, G.750, R.753, R.754 Ligands: MG.2 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.602, A:C.641, A:N.642, A:G.643, A:K.644, A:K.644, A:T.645, A:T.645, A:F.646, A:D.779, B:N.712, B:R.753, B:R.753, B:R.754 pi-Stacking: A:F.764, A:F.764, A:F.782 ANP.3: 19 residues within 4Å: Chain B: A.602, G.640, C.641, N.642, G.643, K.644, T.645, F.646, N.739, F.764, K.777, E.778, D.779, P.780, F.782, I.783 Chain C: R.753, R.754 Ligands: MG.4 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.602, B:C.641, B:N.642, B:N.642, B:G.643, B:K.644, B:K.644, B:K.644, B:T.645, B:F.646, B:N.739, B:E.778, B:D.779, B:P.780, B:F.782, B:I.783, C:R.753, C:R.754 pi-Stacking: B:F.764, B:F.764, B:F.782 ANP.5: 19 residues within 4Å: Chain C: A.602, D.605, G.640, C.641, N.642, G.643, K.644, T.645, F.646, N.739, F.764, K.777, E.778, D.779, P.780, I.783 Chain D: R.753, R.754 Ligands: MG.6 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.605, C:C.641, C:N.642, C:G.643, C:K.644, C:K.644, C:T.645, C:T.645, C:F.646, C:D.779, C:P.780, D:R.753, D:R.754 pi-Stacking: C:F.764, C:F.764, C:F.782 ANP.7: 20 residues within 4Å: Chain D: A.602, G.640, C.641, N.642, G.643, K.644, T.645, F.646, E.695, N.739, F.764, K.777, E.778, D.779, P.780, F.782, I.783 Chain E: R.753, R.754 Ligands: MG.8 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:A.602, D:G.640, D:N.642, D:G.643, D:K.644, D:K.644, D:K.644, D:T.645, D:F.646, D:N.739, D:E.778, D:D.779, D:P.780, D:F.782, D:I.783, E:R.753, E:R.754 pi-Stacking: D:F.764, D:F.764, D:F.782 ANP.9: 13 residues within 4Å: Chain E: A.602, D.605, I.606, C.641, N.642, G.643, F.764, K.777, E.778, D.779, P.780, F.782, I.783 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.605, E:D.605, E:G.643, E:D.779 pi-Stacking: E:F.764, E:F.764, E:F.782, E:F.782 ANP.10: 16 residues within 4Å: Chain A: N.712, R.753, R.754 Chain F: A.602, G.643, K.644, T.645, F.646, E.695, F.764, K.777, E.778, D.779, P.780, F.782, I.783 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:T.645, F:T.645, F:T.645, F:F.646, F:E.695, F:E.778, F:D.779, F:I.783, A:N.712, A:R.753, A:R.754, A:R.754 pi-Stacking: F:F.782

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.645 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.645 MG.4: 3 residues within 4Å: Chain B: T.645 Chain C: N.712 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.645 MG.6: 2 residues within 4Å: Chain C: T.645 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.645 MG.8: 2 residues within 4Å: Chain D: T.645 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.645

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shao, Z. et al., Structures and implications of the C962R protein of African swine fever virus. Nucleic Acids Res. (2023)

Release Date

2023-07-26

Peptides

Putative primase C962R: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Putative primase C962R

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