SMTL ID : 8wwa.1

Structure of AMPPNP-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-covalent)

DA-DA-DA-DA.1: 8 residues within 4Å: Chain A: T.22, T.23, T.24, T.25, T.26 Chain E: K.509, R.513 Chain F: R.513 Protein-ligand interaction information (PLIP) not available

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

ANP.2: 22 residues within 4Å: Chain B: A.600, D.603, I.604, G.637, G.638, C.639, N.640, G.641, K.642, T.643, F.644, F.762, K.775, E.776, D.777, P.778, F.780, I.781 Chain C: N.710, R.751, R.752 Ligands: MG.3 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:A.600, B:C.639, B:N.640, B:G.641, B:K.642, B:K.642, B:T.643, B:F.644, B:D.777, B:F.780, B:I.781, C:R.751, C:R.751, C:R.752 pi-Stacking: B:F.762, B:F.762, B:F.780, B:F.780 ANP.4: 19 residues within 4Å: Chain C: A.600, G.638, C.639, N.640, G.641, K.642, T.643, F.644, N.737, F.762, E.776, D.777, P.778, F.780, I.781 Chain G: N.710, R.751, R.752 Ligands: MG.5 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain G Hydrogen bonds: C:A.600, C:C.639, C:N.640, C:G.641, C:T.643, C:T.643, C:T.643, C:F.644, C:N.737, C:D.777, C:D.777, G:N.710, G:R.751, G:R.751, G:R.752 pi-Stacking: C:F.762, C:F.762, C:F.780, C:F.780 ANP.6: 16 residues within 4Å: Chain D: A.600, C.639, N.640, G.641, K.642, T.643, F.644, F.762, K.775, E.776, D.777, F.780, I.781 Chain E: R.751, R.752 Ligands: MG.7 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:A.600, D:C.639, D:N.640, D:G.641, D:T.643, D:F.644, D:R.647, D:D.777, D:F.780, D:I.781, E:R.751, E:R.751, E:R.752 pi-Stacking: D:F.762, D:F.762, D:F.780, D:F.780 ANP.8: 20 residues within 4Å: Chain E: D.603, I.604, G.637, G.638, C.639, N.640, G.641, K.642, T.643, F.644, F.762, K.775, E.776, D.777, P.778, F.780, I.781 Chain F: K.706, R.751 Ligands: MG.9 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:D.603, E:G.637, E:C.639, E:N.640, E:G.641, E:K.642, E:K.642, E:T.643, E:T.643, E:F.644, E:D.777, E:F.780, E:I.781, F:K.706, F:R.751, F:R.751 pi-Stacking: E:F.762, E:F.762, E:F.780, E:F.780 ANP.10: 20 residues within 4Å: Chain B: R.751 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, K.775, E.776, D.777, P.778, F.780, I.781 Ligands: MG.11 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:A.600, F:G.637, F:C.639, F:N.640, F:G.641, F:K.642, F:K.642, F:K.642, F:T.643, F:F.644, F:N.737, F:D.777, F:F.780, F:I.781, B:R.751, B:R.751 pi-Stacking: F:F.762, F:F.762, F:F.780, F:F.780 ANP.13: 18 residues within 4Å: Chain G: A.600, I.604, G.637, G.638, C.639, N.640, G.641, K.642, T.643, F.644, N.737, F.762, K.775, E.776, D.777, F.780, I.781 Ligands: MG.12 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:A.600, G:C.639, G:N.640, G:G.641, G:K.642, G:K.642, G:K.642, G:T.643, G:F.644, G:N.737, G:D.777, G:F.780, G:I.781 pi-Stacking: G:F.762, G:F.762, G:F.780, G:F.780

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: T.643 Chain C: N.710 Ligands: ANP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.643 MG.5: 4 residues within 4Å: Chain C: K.642, T.643, E.692 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.643 MG.7: 5 residues within 4Å: Chain D: G.641, K.642, T.643, F.644 Ligands: ANP.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: ANP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.643 MG.11: 3 residues within 4Å: Chain F: T.643, F.644 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.643 MG.12: 2 residues within 4Å: Chain G: T.643 Ligands: ANP.13 No protein-ligand interaction detected (PLIP)

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
A

C
B

D
D

E
E

F
F

G
C

Putative primase C962R

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