SMTL ID : 8qbm.1

Retron-Eco1 filament with ADP-ribosylated Effector (full map with 2 segments)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-5-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.119, D.198 Chain X: G.85 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain I: D.198 Chain Z: G.85 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain 1: G.85 Chain Q: D.119, D.198, K.231 No protein-ligand interaction detected (PLIP)

4 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Covalent)

AR6.2: 17 residues within 4Å: Chain D: C.35, G.36, D.38, R.46, P.64, S.100, P.101, G.102, S.103, E.106 Chain P: P.98, F.128, R.132, S.133, F.134, I.135, N.136 9 PLIP interactions: 3 interactions with chain P, 6 interactions with chain D Hydrogen bonds: P:P.98, P:S.133, P:F.134, D:G.36, D:G.36, D:D.38, D:G.102, D:S.103, D:E.106 AR6.3: 17 residues within 4Å: Chain E: C.35, G.36, P.64, S.100, P.101, G.102, S.103, E.106 Chain G: P.98, F.104, Q.124, F.128, K.131, R.132, S.133, F.134, N.136 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain G Hydrogen bonds: E:G.36, E:G.36, E:G.102, E:E.106, G:P.98, G:S.133, G:F.134 pi-Stacking: G:F.128, G:F.128 AR6.4: 18 residues within 4Å: Chain E: P.98, F.104, F.128, K.131, R.132, S.133, F.134, I.135, N.136 Chain G: C.35, G.36, R.46, P.64, S.100, P.101, G.102, S.103, E.106 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain G Hydrogen bonds: E:P.98, E:F.134, G:G.36, G:G.36, G:D.38, G:G.102, G:S.103, G:E.106 pi-Stacking: E:F.128 AR6.6: 19 residues within 4Å: Chain D: P.98, F.104, Q.124, F.128, K.131, R.132, S.133, F.134, I.135, N.136 Chain P: C.35, G.36, P.64, L.96, S.100, P.101, G.102, S.103, E.106 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain P Hydrogen bonds: D:Q.124, D:S.133, D:F.134, P:G.36, P:G.36, P:G.102, P:E.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carabias, A. et al., Retron-Eco1 assembles NAD + -hydrolyzing filaments that provide immunity against bacteriophages. Mol.Cell (2024)

Release Date

2024-06-05

Peptides

Retron Ec86 reverse transcriptase: AHIMQU
Retron Ec86 putative ribosyltransferase/DNA-binding protein: DEFGP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
I

I
K

M
P

Q
U

U
Z

D
E

E
F

F
G

G
H

P
T

Retron Ec86 reverse transcriptase

Retron Ec86 putative ribosyltransferase/DNA-binding protein

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