SMTL ID : 8hrb.1

Structure of tetradecameric RdrA ring in RNA-loading state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain B: I.16, N.22, P.24, D.31, L.32, I.33, R.78, G.79, A.80, G.81, K.82, T.83, T.84, D.221, D.222, R.377 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.22, B:D.31, B:I.33, B:G.79, B:A.80, B:G.81, B:K.82, B:T.83, B:T.83, B:T.84, B:D.222, B:D.222 Salt bridges: B:R.78, B:R.78, B:K.82, B:R.377, B:R.377 ATP.2: 13 residues within 4Å: Chain E: N.22, P.24, D.31, L.32, I.33, R.78, G.79, G.81, K.82, T.83, T.84, D.222, R.377 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.22, E:N.22, E:D.31, E:I.33, E:R.78, E:G.79, E:G.81, E:K.82, E:T.83, E:T.83, E:T.83, E:T.84, E:T.84 Salt bridges: E:K.82, E:R.377, E:R.377, E:R.377, A:K.300 ATP.3: 15 residues within 4Å: Chain D: K.300 Chain F: N.22, D.31, L.32, I.33, R.78, G.81, K.82, T.83, T.84, D.221, D.222, D.224, R.377, M.380 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:D.31, F:I.33, F:R.78, F:G.81, F:K.82, F:T.83, F:T.83, F:T.84, F:T.84 Salt bridges: F:K.82, F:R.377, F:R.377, D:K.300, D:K.300 ATP.4: 15 residues within 4Å: Chain F: K.300 Chain G: N.22, P.24, D.31, L.32, I.33, R.78, G.79, A.80, G.81, K.82, T.83, D.222, D.224, R.377 15 PLIP interactions: 14 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:N.22, G:N.22, G:I.33, G:G.79, G:A.80, G:G.81, G:K.82, G:T.83, G:D.222 Salt bridges: G:R.78, G:K.82, G:K.82, G:R.377, G:R.377, F:K.300 ATP.5: 17 residues within 4Å: Chain I: I.16, N.22, P.24, D.31, L.32, I.33, R.78, G.79, A.80, G.81, K.82, T.83, T.84, D.221, D.222, R.377 Chain J: K.300 19 PLIP interactions: 2 interactions with chain J, 17 interactions with chain I Salt bridges: J:K.300, J:K.300, I:R.78, I:R.78, I:K.82, I:R.377, I:R.377 Hydrogen bonds: I:N.22, I:D.31, I:I.33, I:G.79, I:A.80, I:G.81, I:K.82, I:T.83, I:T.83, I:T.84, I:D.222, I:D.222 ATP.6: 14 residues within 4Å: Chain H: K.300 Chain L: N.22, P.24, D.31, L.32, I.33, R.78, G.79, G.81, K.82, T.83, T.84, D.222, R.377 18 PLIP interactions: 17 interactions with chain L, 1 interactions with chain H Hydrogen bonds: L:N.22, L:N.22, L:D.31, L:I.33, L:R.78, L:G.79, L:G.81, L:K.82, L:T.83, L:T.83, L:T.83, L:T.84, L:T.84 Salt bridges: L:K.82, L:R.377, L:R.377, L:R.377, H:K.300 ATP.7: 16 residues within 4Å: Chain K: K.300 Chain M: N.22, D.31, L.32, I.33, G.79, A.80, G.81, K.82, T.83, T.84, D.221, D.222, D.224, R.377, M.380 14 PLIP interactions: 12 interactions with chain M, 2 interactions with chain K Hydrogen bonds: M:D.31, M:I.33, M:G.81, M:K.82, M:T.83, M:T.83, M:T.84, M:T.84, M:D.224 Salt bridges: M:K.82, M:R.377, M:R.377, K:K.300, K:K.300 ATP.8: 15 residues within 4Å: Chain M: K.300 Chain N: N.22, P.24, D.31, L.32, I.33, R.78, G.79, A.80, G.81, K.82, T.83, D.222, D.224, R.377 15 PLIP interactions: 14 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:N.22, N:N.22, N:I.33, N:G.79, N:A.80, N:G.81, N:K.82, N:T.83, N:D.222 Salt bridges: N:R.78, N:K.82, N:K.82, N:R.377, N:R.377, M:K.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Molecular basis of RADAR anti-phage supramolecular assemblies. Cell (2023)

Release Date

2023-02-01

Peptides

Archaeal ATPase: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
K

C
L

D
M

E
P

F
Q

G
R

H
A

I
B

J
C

K
D

L
E

M
G

N
H

Archaeal ATPase

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