SMTL ID : 8ww7.1

Structure of AMPPNP-Form AsfvPrimPol Dodecamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

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 A: T.22, T.23, T.24, T.25, T.26 Chain D: K.509 Protein-ligand interaction information (PLIP) not available

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

ANP.2: 19 residues within 4Å: Chain B: A.600, I.604, G.638, C.639, N.640, K.642, T.643, F.644, F.762, K.775, E.776, D.777, P.778, F.780, I.781 Chain G: N.710, R.751, R.752 Ligands: MG.3 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain G Hydrogen bonds: B:A.600, B:C.639, B:N.640, B:K.642, B:K.642, B:D.777, B:F.780, B:I.781, G:R.751, G:R.752, G:R.752 pi-Stacking: B:F.762, B:F.762, B:F.780, B:F.780 ANP.4: 20 residues within 4Å: Chain B: G.748, R.751, R.752 Chain C: A.600, I.604, G.638, C.639, N.640, K.642, T.643, F.644, F.762, K.775, E.776, D.777, P.778, R.779, F.780, I.781 Ligands: MG.5 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:A.600, C:C.639, C:N.640, C:K.642, C:K.642, C:K.642, C:K.642, C:T.643, C:D.777, C:R.779, C:F.780, C:I.781, B:R.751, B:R.752, B:R.752 pi-Stacking: C:F.762, C:F.762, C:F.780 Salt bridges: B:R.751 ANP.6: 20 residues within 4Å: Chain C: G.748, R.751, R.752 Chain D: A.600, 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 Ligands: MG.7 17 PLIP interactions: 11 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:A.600, D:C.639, D:N.640, D:K.642, D:K.642, D:N.737, D:D.777, D:D.777, C:G.748, C:R.751, C:R.751, C:R.752, C:R.752 pi-Stacking: D:F.762, D:F.762, D:F.780 Salt bridges: C:R.751 ANP.8: 15 residues within 4Å: Chain D: R.751, R.752 Chain E: A.600, I.604, C.639, N.640, K.642, T.643, R.647, F.762, K.775, E.776, D.777, F.780 Ligands: MG.9 13 PLIP interactions: 3 interactions with chain D, 10 interactions with chain E Hydrogen bonds: D:R.751, D:R.752, D:R.752, E:A.600, E:C.639, E:T.643, E:R.647, E:D.777, E:F.780 pi-Stacking: E:F.762, E:F.762, E:F.780, E:F.780 ANP.10: 19 residues within 4Å: Chain E: G.748, R.751, R.752 Chain F: A.600, I.604, G.638, C.639, N.640, G.641, K.642, T.643, F.644, F.762, K.775, E.776, D.777, F.780, I.781 Ligands: MG.11 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:A.600, F:C.639, F:N.640, F:G.641, F:T.643, F:T.643, F:D.777, F:F.780, F:I.781, E:R.751, E:R.752, E:R.752 pi-Stacking: F:F.762, F:F.762, F:F.780, F:F.780 ANP.12: 19 residues within 4Å: Chain F: G.748, R.751, R.752 Chain G: A.600, I.604, G.638, C.639, N.640, K.642, T.643, F.644, N.737, F.762, K.775, E.776, D.777, F.780, I.781 Ligands: MG.13 17 PLIP interactions: 3 interactions with chain F, 14 interactions with chain G Hydrogen bonds: F:R.751, F:R.752, F:R.752, G:A.600, G:C.639, G:N.640, G:T.643, G:T.643, G:N.737, G:D.777, G:R.779, G:F.780, G:I.781 pi-Stacking: G:F.762, G:F.762, G:F.780, G:F.780 ANP.14: 18 residues within 4Å: Chain H: A.600, I.604, 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 Chain M: N.710, R.751, R.752 17 PLIP interactions: 6 interactions with chain M, 11 interactions with chain H Hydrogen bonds: M:K.706, M:K.706, M:N.710, M:R.751, M:R.752, M:R.752, H:A.600, H:C.639, H:N.640, H:K.642, H:K.642, H:T.643, H:T.643, H:D.777 pi-Stacking: H:F.762, H:F.762, H:F.780 ANP.15: 19 residues within 4Å: Chain H: G.748, R.751, R.752 Chain I: A.600, 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: 11 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:A.600, I:C.639, I:K.642, I:T.643, I:N.737, I:D.777, I:D.777, H:R.751, H:R.752, H:R.752 pi-Stacking: I:F.762, I:F.762, I:F.780, I:F.780 ANP.16: 17 residues within 4Å: Chain I: G.748, R.751, R.752 Chain J: A.600, D.603, I.604, C.639, N.640, K.642, T.643, F.762, K.775, E.776, D.777, P.778, F.780, I.781 19 PLIP interactions: 15 interactions with chain J, 4 interactions with chain I Hydrogen bonds: J:A.600, J:C.639, J:K.642, J:K.642, J:T.643, J:T.643, J:D.777, J:D.777, J:F.780, J:I.781, I:N.710, I:R.751, I:R.752, I:R.752 Salt bridges: J:K.642 pi-Stacking: J:F.762, J:F.762, J:F.780, J:F.780 ANP.17: 18 residues within 4Å: Chain J: N.710, G.748, R.751, R.752 Chain K: A.600, D.603, I.604, C.639, N.640, G.641, K.642, T.643, F.762, E.776, D.777, P.778, F.780, I.781 16 PLIP interactions: 4 interactions with chain J, 12 interactions with chain K Hydrogen bonds: J:N.710, J:R.751, J:R.752, J:R.752, K:A.600, K:D.603, K:C.639, K:K.642, K:T.643, K:T.643, K:E.776, K:D.777, K:F.780, K:I.781 pi-Stacking: K:F.762, K:F.762 ANP.18: 17 residues within 4Å: Chain K: N.710, G.748, R.751, R.752 Chain L: A.600, D.603, I.604, C.639, N.640, K.642, T.643, F.762, K.775, E.776, D.777, F.780, I.781 17 PLIP interactions: 13 interactions with chain L, 4 interactions with chain K Hydrogen bonds: L:A.600, L:I.604, L:C.639, L:K.642, L:K.642, L:T.643, L:T.643, L:D.777, L:D.777, L:F.780, K:N.710, K:R.751, K:R.752, K:R.752 pi-Stacking: L:F.762, L:F.762, L:F.780 ANP.19: 18 residues within 4Å: Chain L: N.710, G.748, R.751, R.752 Chain M: A.600, D.603, I.604, C.639, N.640, K.642, T.643, N.737, F.762, K.775, E.776, D.777, F.780, I.781 19 PLIP interactions: 15 interactions with chain M, 4 interactions with chain L Hydrogen bonds: M:A.600, M:D.603, M:C.639, M:N.640, M:K.642, M:K.642, M:T.643, M:T.643, M:N.737, M:D.777, M:D.777, M:F.780, M:I.781, L:N.710, L:R.751, L:R.752, L:R.752 pi-Stacking: M:F.762, M:F.762

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain B: N.640, K.642, T.643, F.644 Ligands: ANP.2 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:K.642, B:T.643 MG.5: 3 residues within 4Å: Chain C: K.642, T.643 Ligands: ANP.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:K.642, C:T.643 MG.7: 5 residues within 4Å: Chain D: N.640, G.641, K.642, T.643 Ligands: ANP.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:N.640, D:K.642 MG.9: 5 residues within 4Å: Chain E: N.640, G.641, K.642, T.643 Ligands: ANP.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:N.640, E:K.642 MG.11: 4 residues within 4Å: Chain F: G.641, K.642, T.643 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.643 MG.13: 5 residues within 4Å: Chain G: G.641, K.642, T.643, F.644 Ligands: ANP.12 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:K.642, G:T.643, 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: BCDEFGHIJKLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
L

J
K

K
J

L
I

M
H

Putative primase C962R

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