SMTL ID : 8fug.1

Alzheimer's disease paired-helical filament in complex with PET tracer GTP-1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-23-mer

Ligands

23 x Y9H: (5S)-2-[4-(2-fluoroethyl)piperidin-1-yl]pyrimido[1,2-a]benzimidazole(Non-covalent)

Y9H.1: 8 residues within 4Å: Chain A: Q.46, S.47, K.48, I.55 Chain C: Q.46, S.47, K.48 Ligands: Y9H.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.48 Y9H.2: 8 residues within 4Å: Chain B: Q.46, S.47, K.48, I.55 Chain D: Q.46, S.47, K.48 Ligands: Y9H.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.48 Y9H.3: 12 residues within 4Å: Chain A: K.48, D.53, I.55 Chain C: Q.46, S.47, K.48, I.55 Chain E: Q.46, S.47, K.48 Ligands: Y9H.1, Y9H.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.55 Hydrogen bonds: C:K.48 Y9H.4: 12 residues within 4Å: Chain B: K.48, D.53, I.55 Chain D: Q.46, S.47, K.48, I.55 Chain F: Q.46, S.47, K.48 Ligands: Y9H.2, Y9H.6 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.48, B:D.53 Hydrophobic interactions: B:I.55 Y9H.5: 12 residues within 4Å: Chain C: K.48, D.53, I.55 Chain E: Q.46, S.47, K.48, I.55 Chain G: Q.46, S.47, K.48 Ligands: Y9H.3, Y9H.7 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:I.55 Hydrogen bonds: E:K.48 Y9H.6: 12 residues within 4Å: Chain D: K.48, D.53, I.55 Chain F: Q.46, S.47, K.48, I.55 Chain H: Q.46, S.47, K.48 Ligands: Y9H.4, Y9H.8 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:I.55 Hydrogen bonds: D:D.53, F:K.48 Y9H.7: 12 residues within 4Å: Chain E: K.48, D.53, I.55 Chain G: Q.46, S.47, K.48, I.55 Chain I: Q.46, S.47, K.48 Ligands: Y9H.5, Y9H.9 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:I.55 Hydrogen bonds: G:K.48 Y9H.8: 12 residues within 4Å: Chain F: K.48, D.53, I.55 Chain H: Q.46, S.47, K.48, I.55 Chain J: Q.46, S.47, K.48 Ligands: Y9H.6, Y9H.10 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain F Hydrogen bonds: H:K.48, F:D.53 Hydrophobic interactions: F:I.55 Y9H.9: 12 residues within 4Å: Chain G: K.48, D.53, I.55 Chain I: Q.46, S.47, K.48, I.55 Chain K: Q.46, S.47, K.48 Ligands: Y9H.7, Y9H.11 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:K.48 Hydrophobic interactions: G:I.55 Y9H.10: 12 residues within 4Å: Chain H: K.48, D.53, I.55 Chain J: Q.46, S.47, K.48, I.55 Chain L: Q.46, S.47, K.48 Ligands: Y9H.8, Y9H.12 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain J Hydrophobic interactions: H:I.55 Hydrogen bonds: H:D.53, J:K.48 Y9H.11: 12 residues within 4Å: Chain I: K.48, D.53, I.55 Chain K: Q.46, S.47, K.48, I.55 Chain M: Q.46, S.47, K.48 Ligands: Y9H.9, Y9H.13 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain K Hydrophobic interactions: I:I.55 Hydrogen bonds: K:K.48 Y9H.12: 12 residues within 4Å: Chain J: K.48, D.53, I.55 Chain L: Q.46, S.47, K.48, I.55 Chain N: Q.46, S.47, K.48 Ligands: Y9H.10, Y9H.14 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: J:I.55 Hydrogen bonds: J:D.53, L:K.48 Y9H.13: 12 residues within 4Å: Chain K: K.48, D.53, I.55 Chain M: Q.46, S.47, K.48, I.55 Chain O: Q.46, S.47, K.48 Ligands: Y9H.11, Y9H.15 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain K Hydrogen bonds: M:K.48 Hydrophobic interactions: K:I.55 Y9H.14: 12 residues within 4Å: Chain L: K.48, D.53, I.55 Chain N: Q.46, S.47, K.48, I.55 Chain P: Q.46, S.47, K.48 Ligands: Y9H.12, Y9H.16 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain N Hydrophobic interactions: L:I.55 Hydrogen bonds: L:D.53, N:K.48 Y9H.15: 12 residues within 4Å: Chain M: K.48, D.53, I.55 Chain O: Q.46, S.47, K.48, I.55 Chain Q: Q.46, S.47, K.48 Ligands: Y9H.13, Y9H.17 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain M Hydrogen bonds: O:K.48 Hydrophobic interactions: M:I.55 Y9H.16: 12 residues within 4Å: Chain N: K.48, D.53, I.55 Chain P: Q.46, S.47, K.48, I.55 Chain R: Q.46, S.47, K.48 Ligands: Y9H.14, Y9H.18 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain P Hydrophobic interactions: N:I.55 Hydrogen bonds: N:D.53, P:K.48 Y9H.17: 12 residues within 4Å: Chain O: K.48, D.53, I.55 Chain Q: Q.46, S.47, K.48, I.55 Chain S: Q.46, S.47, K.48 Ligands: Y9H.15, Y9H.19 3 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain O Hydrogen bonds: Q:K.48, O:D.53 Hydrophobic interactions: O:I.55 Y9H.18: 12 residues within 4Å: Chain P: K.48, D.53, I.55 Chain R: Q.46, S.47, K.48, I.55 Chain T: Q.46, S.47, K.48 Ligands: Y9H.16, Y9H.20 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain R Hydrophobic interactions: P:I.55 Hydrogen bonds: R:K.48 Y9H.19: 12 residues within 4Å: Chain Q: K.48, D.53, I.55 Chain S: Q.46, S.47, K.48, I.55 Chain U: Q.46, S.47, K.48 Ligands: Y9H.17, Y9H.21 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain S Hydrophobic interactions: Q:I.55 Hydrogen bonds: S:K.48 Y9H.20: 12 residues within 4Å: Chain R: K.48, D.53, I.55 Chain T: Q.46, S.47, K.48, I.55 Chain V: Q.46, S.47, K.48 Ligands: Y9H.18, Y9H.22 3 PLIP interactions: 2 interactions with chain R, 1 interactions with chain T Hydrophobic interactions: R:I.55 Hydrogen bonds: R:D.53, T:K.48 Y9H.21: 12 residues within 4Å: Chain S: K.48, D.53, I.55 Chain U: Q.46, S.47, K.48, I.55 Chain W: Q.46, S.47, K.48 Ligands: Y9H.19, Y9H.23 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain S Hydrogen bonds: U:K.48 Hydrophobic interactions: S:I.55 Y9H.22: 8 residues within 4Å: Chain T: K.48, D.53, I.55 Chain V: Q.46, S.47, K.48, I.55 Ligands: Y9H.20 3 PLIP interactions: 2 interactions with chain T, 1 interactions with chain V Hydrophobic interactions: T:I.55 Hydrogen bonds: T:D.53, V:K.48 Y9H.23: 8 residues within 4Å: Chain U: K.48, D.53, I.55 Chain W: Q.46, S.47, K.48, I.55 Ligands: Y9H.21 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W Hydrophobic interactions: U:I.55 Hydrogen bonds: W:K.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Merz, G.E. et al., Stacked binding of a PET ligand to Alzheimer's tau paired helical filaments. Nat Commun (2023)

Release Date

2023-06-07

Peptides

Microtubule-associated protein tau: ABCDEFGHIJKLMNOPQRSTUVW

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

Microtubule-associated protein tau

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