SMTL ID : 8ww9.1

Structure of ADP-Form AsfvPrimPol Dodecamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

DA-DA-DA.1: 6 residues within 4Å: Chain A: T.1, T.2, T.3, T.4, T.5, T.6 2 PLIP interactions: 2 interactions with chain J Salt bridges: J:R.513, J:R.513 DA-DA-DA.2: 6 residues within 4Å: Chain C: K.509 Chain N: T.25, T.26, T.27, T.28, T.29 Protein-ligand interaction information (PLIP) not available

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

ADP.3: 15 residues within 4Å: Chain B: A.600, G.638, C.639, N.640, K.642, T.643, E.693, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:A.600, B:C.639, B:N.640, B:T.643, B:T.643, B:E.693, B:E.693, B:N.737, B:E.776, B:D.777, B:P.778, B:F.780, B:I.781 Salt bridges: B:K.642 pi-Stacking: B:F.762, B:F.780 ADP.4: 17 residues within 4Å: Chain C: A.600, D.603, I.604, G.638, C.639, N.640, K.642, T.643, E.693, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:A.600, C:C.639, C:N.640, C:T.643, C:T.643, C:E.693, C:E.693, C:E.693, C:E.776, C:D.777, C:P.778, C:I.781 Salt bridges: C:K.642 pi-Stacking: C:F.780 ADP.5: 16 residues within 4Å: Chain D: A.600, D.603, I.604, G.638, C.639, N.640, K.642, T.643, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:A.600, D:C.639, D:N.640, D:T.643, D:T.643, D:N.737, D:E.776, D:D.777 pi-Stacking: D:F.762, D:F.762, D:F.780, D:F.780 ADP.6: 15 residues within 4Å: Chain E: A.600, I.604, G.638, C.639, N.640, K.642, T.643, E.693, F.762, K.775, E.776, D.777, P.778, F.780, I.781 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:A.600, E:C.639, E:N.640, E:K.642, E:T.643, E:E.693, E:E.693, E:E.693, E:E.776, E:D.777, E:P.778, E:F.780, E:I.781 Salt bridges: E:K.642 pi-Stacking: E:F.780 ADP.7: 16 residues within 4Å: Chain F: A.600, I.604, G.638, C.639, N.640, K.642, T.643, E.693, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:A.600, F:C.639, F:N.640, F:T.643, F:T.643, F:E.693, F:E.693, F:E.693, F:N.737, F:E.776, F:D.777, F:P.778, F:F.780, F:I.781 Salt bridges: F:K.642 pi-Stacking: F:F.780, F:F.780 ADP.8: 15 residues within 4Å: Chain G: A.600, I.604, G.638, C.639, N.640, K.642, T.643, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:A.600, G:C.639, G:N.640, G:T.643, G:T.643, G:N.737, G:D.777, G:I.781 pi-Stacking: G:F.780, G:F.780 ADP.9: 16 residues within 4Å: Chain H: A.600, D.603, I.604, C.639, N.640, G.641, K.642, T.643, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:C.639, H:N.640, H:T.643, H:N.737, H:N.737, H:D.777, H:I.781 Salt bridges: H:K.642 pi-Stacking: H:F.762, H:F.762, H:F.780 ADP.10: 19 residues within 4Å: Chain I: A.600, D.603, I.604, G.638, C.639, N.640, K.642, T.643, F.644, E.693, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 Chain J: R.751 17 PLIP interactions: 14 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:A.600, I:C.639, I:N.640, I:T.643, I:E.693, I:E.693, I:N.737, I:D.777, I:F.780, I:I.781, J:R.751, J:R.751 Salt bridges: I:K.642, J:R.751 pi-Stacking: I:F.762, I:F.762, I:F.780 ADP.11: 17 residues within 4Å: Chain J: A.600, D.603, I.604, C.639, N.640, G.641, K.642, T.643, E.693, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:C.639, J:T.643, J:E.693, J:E.693, J:N.737, J:D.777, J:P.778, J:F.780, J:I.781 pi-Stacking: J:F.762, J:F.762, J:F.780 ADP.12: 17 residues within 4Å: Chain K: A.600, D.603, I.604, C.639, N.640, G.641, K.642, T.643, F.644, E.693, F.762, K.775, E.776, D.777, P.778, F.780, I.781 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:D.603, K:I.604, K:C.639, K:N.640, K:T.643, K:E.693, K:E.693, K:D.777, K:I.781 pi-Stacking: K:F.644, K:F.762, K:F.762 ADP.13: 17 residues within 4Å: Chain L: A.600, D.603, I.604, C.639, N.640, G.641, K.642, T.643, F.644, E.693, N.737, F.762, E.776, D.777, P.778, F.780, I.781 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:I.604, L:C.639, L:T.643, L:E.693, L:E.693, L:E.693, L:N.737, L:D.777, L:I.781 pi-Stacking: L:F.762, L:F.780 ADP.14: 18 residues within 4Å: Chain H: R.752 Chain M: A.600, D.603, I.604, G.638, C.639, N.640, K.642, T.643, F.644, N.737, F.762, K.775, E.776, D.777, P.778, F.780, I.781 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain H Hydrogen bonds: M:A.600, M:I.604, M:C.639, M:N.640, M:N.737, M:N.737, M:D.777, M:D.777, H:R.752 Salt bridges: M:K.642 pi-Stacking: M:F.644, M:F.762, M:F.762, M:F.780

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: BCDEFGHIJKLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

J
I

K
J

L
K

M
L

Putative primase C962R

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