SMTL ID : 8wvz.1

Structure of ADP-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: 6 residues within 4Å: Chain F: R.513 Chain G: T.21, T.22, T.23, T.24, T.25 Protein-ligand interaction information (PLIP) not available

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 14 residues within 4Å: Chain A: A.600, I.604, G.638, C.639, N.640, G.641, T.643, F.762, E.776, D.777, F.780, I.781 Chain B: R.751 Ligands: MG.3 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.600, A:F.644, A:D.777, A:D.777, A:D.777, A:F.780, B:R.751 pi-Stacking: A:F.762, A:F.762, A:F.780, A:F.780 ADP.4: 16 residues within 4Å: Chain B: A.600, 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.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.638, B:N.640, B:G.641, B:K.642, B:T.643, B:F.644, B:D.777, B:D.777 pi-Stacking: B:F.780, B:F.780 ADP.6: 18 residues within 4Å: Chain C: A.600, 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 D: R.751 Ligands: MG.7 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.600, C:G.637, C:N.640, C:G.641, C:K.642, C:T.643, C:T.643, C:F.644, C:E.693, C:D.777, C:P.778, C:I.781, D:R.751 ADP.8: 16 residues within 4Å: Chain D: A.600, I.604, G.638, C.639, N.640, G.641, K.642, T.643, F.644, F.762, E.776, D.777, P.778, F.780, I.781 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:A.600, D:G.638, D:G.638, D:N.640, D:G.641, D:K.642, D:T.643, D:F.644, D:D.777, D:D.777 pi-Stacking: D:F.762 ADP.10: 16 residues within 4Å: Chain E: A.600, 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 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:A.600, E:G.638, E:G.638, E:G.641, E:K.642, E:T.643, E:T.643, E:F.644, E:D.777, E:I.781 pi-Stacking: E:F.644, E:F.762, E:F.762 ADP.12: 17 residues within 4Å: Chain A: R.751 Chain F: A.600, I.604, G.638, C.639, N.640, G.641, K.642, T.643, F.644, F.762, E.776, D.777, P.778, F.780, I.781 Ligands: MG.13 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:A.600, F:G.641, F:T.643, F:T.643, F:T.643, F:F.644, F:R.647, F:D.777, F:P.778, F:I.781 pi-Stacking: F:F.762, F:F.780 Salt bridges: A:R.751

6 x MG: MAGNESIUM ION(Non-covalent)

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

2024-10-30

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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