- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-1-1-1-6-mer
- Ligands
- 1 x ZN: ZINC ION(Non-covalent)
- 7 x MG: MAGNESIUM ION(Non-covalent)
- 6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.3: 14 residues within 4Å:- Chain F: D.163, P.188, K.189, A.190, G.191, K.192, T.193, T.194, K.198, E.359, F.364
- Chain G: R.375
- Ligands: MG.4, BEF.5
18 PLIP interactions:15 interactions with chain F, 3 interactions with chain G- Hydrogen bonds: F:D.163, F:D.163, F:P.187, F:K.189, F:A.190, F:G.191, F:K.192, F:T.193, F:T.193, F:T.194, F:K.198, G:R.375
- Salt bridges: F:K.192, F:K.192, G:R.375, G:R.375
- pi-Stacking: F:F.364, F:F.364
ADP.6: 13 residues within 4Å:- Chain G: P.188, K.189, A.190, G.191, K.192, T.193, T.194, K.198, E.359, F.364
- Chain H: R.375
- Ligands: MG.7, BEF.8
15 PLIP interactions:14 interactions with chain G, 1 interactions with chain H- Hydrogen bonds: G:K.189, G:A.190, G:G.191, G:K.192, G:T.193, G:T.193, G:T.194, G:K.198, G:K.198, G:E.359
- Salt bridges: G:K.192, G:R.220, H:R.375
- pi-Stacking: G:F.364, G:F.364
ADP.9: 13 residues within 4Å:- Chain H: P.187, P.188, K.189, A.190, G.191, K.192, T.193, T.194, K.198, E.359, F.364
- Ligands: MG.10, BEF.11
12 PLIP interactions:12 interactions with chain H- Hydrogen bonds: H:K.189, H:A.190, H:G.191, H:K.192, H:T.193, H:T.193, H:K.198, H:K.198, H:E.359
- Salt bridges: H:K.192
- pi-Stacking: H:F.364, H:F.364
ADP.12: 13 residues within 4Å:- Chain I: P.187, P.188, K.189, A.190, G.191, K.192, T.193, T.194, K.198, E.359, F.364
- Ligands: MG.13, BEF.14
14 PLIP interactions:14 interactions with chain I- Hydrogen bonds: I:D.163, I:K.189, I:A.190, I:G.191, I:K.192, I:T.193, I:T.193, I:T.194, I:T.194, I:K.198, I:E.359
- Salt bridges: I:K.192
- pi-Stacking: I:F.364, I:F.364
ADP.15: 14 residues within 4Å:- Chain J: P.187, P.188, K.189, A.190, G.191, K.192, T.193, T.194, K.198, E.359, F.364
- Chain K: R.375
- Ligands: MG.16, BEF.17
13 PLIP interactions:12 interactions with chain J, 1 interactions with chain K- Hydrogen bonds: J:K.189, J:A.190, J:G.191, J:K.192, J:T.193, J:T.194, J:T.194, J:K.198, J:E.359
- Salt bridges: J:K.192, K:R.375
- pi-Stacking: J:F.364, J:F.364
ADP.18: 13 residues within 4Å:- Chain F: R.375
- Chain K: P.188, K.189, A.190, G.191, K.192, T.193, T.194, K.198, E.359, F.364
- Ligands: MG.19, BEF.20
17 PLIP interactions:13 interactions with chain K, 4 interactions with chain F- Hydrogen bonds: K:K.189, K:A.190, K:G.191, K:K.192, K:T.193, K:T.193, K:T.194, K:T.194, K:K.198, F:R.375, F:R.375
- Salt bridges: K:K.192, K:R.220, F:R.375, F:R.375
- pi-Stacking: K:F.364, K:F.364
- 6 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)
BEF.5: 8 residues within 4Å:- Chain F: P.188, K.189, K.192, T.193, R.220, L.329
- Ligands: ADP.3, MG.4
No protein-ligand interaction detected (PLIP)BEF.8: 9 residues within 4Å:- Chain G: P.188, K.189, K.192, E.219, R.220
- Chain H: G.346, R.375
- Ligands: ADP.6, MG.7
No protein-ligand interaction detected (PLIP)BEF.11: 6 residues within 4Å:- Chain H: P.188, K.189, K.192, R.220
- Ligands: ADP.9, MG.10
No protein-ligand interaction detected (PLIP)BEF.14: 6 residues within 4Å:- Chain I: P.188, K.189, K.192, R.220
- Ligands: ADP.12, MG.13
No protein-ligand interaction detected (PLIP)BEF.17: 7 residues within 4Å:- Chain J: P.188, K.189, K.192, R.220
- Chain K: R.375
- Ligands: ADP.15, MG.16
No protein-ligand interaction detected (PLIP)BEF.20: 7 residues within 4Å:- Chain K: P.188, K.189, K.192, R.220, L.329
- Ligands: ADP.18, MG.19
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Murayama, Y. et al., Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. Sci Adv (2023)
- Release Date
- 2023-05-03
- Peptides
- DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
Transcription termination factor Rho: FGHIJK - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
HC
ID
JE
KF
AG
BH
CI
DJ
EK
F
SMTL ID : 8hsl.1
Thermus thermophilus RNA polymerase bound with an inverted Rho hexamer
DNA-directed RNA polymerase subunit alpha
Toggle Identical (AB)DNA-directed RNA polymerase subunit beta
DNA-directed RNA polymerase subunit beta'
DNA-directed RNA polymerase subunit omega
Transcription termination factor Rho
Toggle Identical (FGHIJK)Related Entries With Identical Sequence
1iw7.1 | 1iw7.2 | 1smy.1 | 1smy.2 | 1zyr.1 | 1zyr.2 | 2a68.1 | 2a68.2 | 2a69.1 | 2a69.2 | 2a6e.1 | 2a6e.2 | 2a6h.1 | 2a6h.2 | 2be5.1 | 2be5.2 | 2cw0.1 | 2cw0.2 | 2o5i.1 | 2o5i.2 | 2o5j.1 | 2o5j.2 | 2ppb.1 | 2ppb.2 | 3aoh.1 | 3aoh.2 | 3aoh.3 | 3aoi.1 | 3aoi.2 | 3aoi.3 more...less...3dxj.1 | 3dxj.2 | 3eql.1 | 3eql.2 | 3wod.1 | 4g7h.1 | 4g7h.2 | 4g7o.1 | 4g7o.2 | 4g7z.1 | 4g7z.2 | 4gzy.1 | 4gzz.1 | 4mq9.1 | 4oin.1 | 4oio.1 | 4oip.1 | 4oiq.1 | 4oir.1 | 4q4z.1 | 4q5s.1 | 4wqs.1 | 4wqs.2 | 4wqt.1 | 4wqt.2 | 4wqt.3 | 5d4c.1 | 5d4c.2 | 5d4d.1 | 5d4d.2 | 5d4e.1 | 5d4e.2 | 5e17.1 | 5e18.1 | 5i2d.1 | 5i2d.2 | 5tmc.1 | 5tmf.1 | 5vo8.1 | 5voi.1 | 5x21.1 | 5x22.1 | 5x22.2 | 5xj0.1 | 6asg.1 | 6cuu.1 | 6kqd.1 | 6kqd.2 | 6kqe.1 | 6kqf.1 | 6kqg.1 | 6kqh.1 | 6kql.1 | 6kqm.1 | 6kqn.1 | 6l74.1 | 6lts.1 | 6m6a.1 | 6m6b.1 | 6m6c.1 | 6ovr.1 | 6ovy.1 | 6ow3.1 | 6oy5.1 | 6oy6.1 | 6oy7.1 | 6p70.1 | 6p71.1 | 6wox.1 | 6woy.1 | 7eh0.1 | 7eh1.1 | 7eh2.1 | 7eh2.2 | 7mlb.1 | 7mli.1 | 7mlj.1 | 7rdq.1 | 8hsg.1 | 8hsh.1 | 8hsj.1 | 8hsr.1 | 8w8n.1 | 8w8o.1 | 8w8p.1