SMTL ID : 8ptm.1

Structure of the transcription termination factor Rho in complex with Rof and ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-5-mer

Ligands

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

ADP.1: 12 residues within 4Å: Chain B: R.366, E.369 Chain C: P.179, P.180, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.2 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.181, C:A.182, C:G.183, C:K.184, C:T.185, C:T.185, C:M.186 Salt bridges: C:K.184, B:R.366 pi-Stacking: C:F.355, C:F.355 ADP.3: 9 residues within 4Å: Chain C: E.369 Chain D: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.4 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.158, D:K.181, D:A.182, D:G.183, D:K.184, D:T.185, C:E.369 Salt bridges: D:K.181 pi-Stacking: D:F.355, D:F.355 ADP.5: 11 residues within 4Å: Chain D: R.366, K.367, E.369 Chain E: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:K.181, E:A.182, E:G.183, E:K.184, E:T.185, E:M.186, E:R.212, D:K.367, D:E.369 Salt bridges: E:K.184, D:R.366 pi-Stacking: E:F.355

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: K.184, T.185 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.185 MG.4: 2 residues within 4Å: Chain D: T.185 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Said, N. et al., Sm-like protein Rof inhibits transcription termination factor rho by binding site obstruction and conformational insulation. Nat Commun (2024)

Release Date

2024-04-17

Peptides

Transcription termination factor Rho: ABCDEF
Protein rof: GHIJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
a

H
b

I
c

J
d

K
e

Transcription termination factor Rho

Protein rof

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