SMTL ID : 8ww6.1

Structure of ATP-rs-Form AsfvPrimPol Hexamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

1 x DA- DA- DA- DA: DNA (5'-D(P*AP*AP*AP*A)-3')(Non-functional Binders)

DA-DA-DA-DA.1: 5 residues within 4Å: Chain A: T.21, T.22, T.23, T.24, T.25 Protein-ligand interaction information (PLIP) not available

6 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 15 residues within 4Å: Chain B: A.600, I.604, G.638, C.639, N.640, G.641, K.642, T.643, F.762, E.776, D.777, F.780, I.781 Chain D: R.752 Ligands: MG.3 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:A.600, B:N.640, B:G.641, B:K.642, B:T.643, B:F.644, B:D.777, B:D.777, D:R.752 pi-Stacking: B:F.762, B:F.780 AGS.4: 14 residues within 4Å: Chain B: R.751 Chain C: A.600, C.639, N.640, G.641, K.642, T.643, F.762, K.775, E.776, D.777, F.780, I.781 Ligands: MG.5 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.600, C:G.641, C:K.642, C:T.643, C:D.777, C:F.780, C:I.781, B:R.751 pi-Stacking: C:F.762, C:F.780 Salt bridges: B:R.751 AGS.6: 15 residues within 4Å: Chain D: A.600, G.637, G.638, C.639, N.640, G.641, K.642, T.643, E.693, F.762, E.776, D.777, F.780, I.781 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.600, D:N.640, D:G.641, D:K.642, D:T.643, D:N.737, D:D.777 pi-Stacking: D:F.762, D:F.780 AGS.8: 16 residues within 4Å: Chain E: A.600, I.604, G.638, C.639, N.640, G.641, K.642, T.643, E.693, N.737, F.762, E.776, D.777, P.778, F.780 Ligands: MG.9 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:A.600, E:N.640, E:G.641, E:K.642, E:T.643, E:N.737, E:D.777 pi-Stacking: E:F.762, E:F.780 AGS.10: 17 residues within 4Å: Chain F: A.600, D.603, I.604, G.637, G.638, C.639, N.640, G.641, K.642, T.643, F.644, F.762, E.776, D.777, F.780, I.781 Ligands: MG.11 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:A.600, F:N.640, F:G.641, F:K.642, F:T.643, F:F.644, F:D.777, F:F.780, F:I.781 pi-Stacking: F:F.780 AGS.12: 15 residues within 4Å: Chain G: A.600, I.604, G.638, C.639, N.640, G.641, K.642, T.643, F.762, K.775, E.776, D.777, F.780, I.781 Ligands: MG.13 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:A.600, G:G.641, G:K.642, G:T.643, G:F.644, G:D.777, G:F.780 pi-Stacking: G:F.762

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: T.643 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.643 MG.5: 5 residues within 4Å: Chain C: G.641, K.642, T.643, F.644 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.643 MG.7: 2 residues within 4Å: Chain D: T.643 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.643 MG.9: 2 residues within 4Å: Chain E: T.643 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.643 MG.11: 2 residues within 4Å: Chain F: T.643 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.643 MG.13: 2 residues within 4Å: Chain G: T.643 Ligands: AGS.12 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.643

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, T.H. et al., Structure of ADP-Form AsfvPrimPol Hexamer. To Be Published

Release Date

2025-04-30

Peptides

Putative primase C962R: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

C
A

D
C

E
D

F
E

G
F

Putative primase C962R

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