SMTL ID : 8q3n.1

Bacterial transcription termination factor Rho + ADP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 11 residues within 4Å: Chain A: T.158, P.179, P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.353, F.355 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.181, A:A.182, A:G.183, A:K.184, A:T.185, A:T.185, A:R.353, A:R.353 Salt bridges: A:K.184, A:K.184 pi-Stacking: A:F.355 ADP.2: 12 residues within 4Å: Chain A: R.366, E.369 Chain B: T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.353, F.355 Ligands: MG.3 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.158, B:K.181, B:A.182, B:G.183, B:K.184, B:T.185, B:T.185, B:M.186, B:R.353, A:R.366, A:E.369 Salt bridges: B:K.184, A:R.366 pi-Stacking: B:F.355 ADP.4: 11 residues within 4Å: Chain B: R.366, E.369 Chain C: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.5 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:T.158, C:T.158, C:K.181, C:A.182, C:G.183, C:K.184, C:T.185, C:M.186, B:R.366, B:E.369 Salt bridges: C:K.184, B:R.366 pi-Stacking: C:F.355 ADP.6: 12 residues within 4Å: Chain C: R.366, E.369 Chain D: T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.353, F.355 Ligands: MG.7 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.158, D:T.158, D:K.181, D:A.182, D:G.183, D:K.184, D:T.185, D:T.185, D:M.186, D:R.353, C:R.366, C:E.369 Salt bridges: D:K.184, C:R.366 pi-Stacking: D:F.355 ADP.8: 10 residues within 4Å: Chain D: R.366, E.369 Chain E: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.9 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.181, E:A.182, E:G.183, E:K.184, E:T.185, E:T.185, E:M.186 Salt bridges: E:K.184, D:R.366 pi-Stacking: E:F.355 ADP.10: 9 residues within 4Å: Chain E: K.367, E.369 Chain F: K.181, A.182, G.183, K.184, T.185, M.186, F.355 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:K.181, F:A.182, F:G.183, F:K.184, F:T.185, F:T.185, F:T.185, F:M.186, E:K.367, E:E.369 Salt bridges: F:K.184 pi-Stacking: F:F.355, F:F.355

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: T.185 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.185 MG.5: 3 residues within 4Å: Chain C: T.185, R.212 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.185 MG.7: 2 residues within 4Å: Chain D: T.185 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.185 MG.9: 2 residues within 4Å: Chain E: T.185 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Transcription termination factor rho polymerizes under stress. Biorxiv (2023)

Release Date

2023-09-27

Peptides

Transcription termination factor Rho: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Transcription termination factor Rho

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