SMTL ID : 8hsj.1

Thermus thermophilus transcription termination factor Rho bound with ADP-BeF3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: P.188, K.189, G.191, K.192, T.193, T.194, L.195, K.198, E.219, R.220, E.223, S.275, L.329, F.364 Chain B: R.375 Ligands: MG.2, BEF.3 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.189, A:G.191, A:K.192, A:T.193, A:T.193, A:T.194, A:T.194, A:L.195, A:K.198, A:E.219, A:E.219, A:R.220, B:R.375 Salt bridges: A:K.192, A:K.192, A:R.220 ADP.4: 18 residues within 4Å: Chain B: G.191, K.192, T.193, T.194, L.195, K.198, E.219, R.220, E.223, D.274, S.275, R.278, L.329, F.364 Chain C: G.346, R.375 Ligands: MG.5, BEF.6 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.191, B:T.193, B:T.194, B:T.194, B:L.195, B:K.198, B:E.219, B:E.223, B:S.275, C:R.375 Salt bridges: B:K.192, B:K.192, B:R.220, B:R.220, B:R.278 ADP.7: 17 residues within 4Å: Chain C: G.191, K.192, T.193, T.194, K.198, E.219, R.220, E.223, D.274, S.275, R.278, T.327, L.329, F.364 Chain D: R.375 Ligands: MG.8, BEF.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.193, C:T.194, C:T.194, C:L.195, C:K.198, C:E.223, C:E.223, C:T.327 Salt bridges: C:K.192, C:K.192, C:R.220, C:R.278 ADP.10: 18 residues within 4Å: Chain D: K.189, G.191, K.192, T.193, T.194, L.195, K.198, E.219, R.220, E.223, D.274, S.275, T.327, L.329, F.364 Chain E: R.375 Ligands: MG.11, BEF.12 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.191, D:K.192, D:T.193, D:T.193, D:T.194, D:L.195, D:K.198, D:R.220, D:E.223, D:E.223, D:D.274, D:T.327 Salt bridges: D:K.192, D:K.192 ADP.13: 16 residues within 4Å: Chain E: G.191, K.192, T.193, T.194, E.219, R.220, E.223, D.274, S.275, R.278, T.327, L.329, F.364 Chain F: R.375 Ligands: MG.14, BEF.15 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.191, E:G.191, E:T.193, E:T.193, E:T.194, E:L.195, E:E.219, E:E.223, E:E.223, E:D.274, E:R.278, E:T.327, F:R.375 Salt bridges: E:K.192, E:K.192 ADP.16: 18 residues within 4Å: Chain A: R.375 Chain F: K.189, G.191, K.192, T.193, T.194, L.195, K.198, E.219, R.220, E.223, D.274, S.275, R.278, L.329, F.364 Ligands: MG.17, BEF.18 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.191, F:K.192, F:T.193, F:T.193, F:T.194, F:T.194, F:L.195, F:K.198, F:E.223, F:D.274, A:R.375 Salt bridges: F:K.192, F:K.192, F:R.220, F:R.220, F:R.278

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.193, R.220, E.223 Chain B: R.375 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.193, A:E.223 MG.5: 5 residues within 4Å: Chain B: G.191, K.192, T.193 Ligands: ADP.4, BEF.6 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain C: T.193, E.219, R.220, E.223 Ligands: ADP.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.193, C:E.219, C:E.223 MG.11: 6 residues within 4Å: Chain D: T.193, E.219, R.220, E.223 Ligands: ADP.10, BEF.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.219 MG.14: 4 residues within 4Å: Chain E: K.192, T.193 Ligands: ADP.13, BEF.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.193 MG.17: 5 residues within 4Å: Chain A: R.375 Chain F: T.193, R.220, E.223 Ligands: ADP.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.193, F:E.223

6 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 8 residues within 4Å: Chain A: P.188, K.189, K.192, R.220, L.329 Chain B: G.346, R.375 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) BEF.6: 8 residues within 4Å: Chain B: P.187, P.188, K.189, A.190, G.191, K.192 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.9: 7 residues within 4Å: Chain C: P.188, K.189, A.190, K.192, R.220 Chain D: R.375 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) BEF.12: 8 residues within 4Å: Chain D: P.188, K.189, K.192, R.278, L.329 Chain E: R.375 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 7 residues within 4Å: Chain E: P.188, K.189, A.190, K.192 Chain F: R.375 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) BEF.18: 8 residues within 4Å: Chain A: R.375 Chain F: P.187, P.188, K.189, K.192, R.278, L.329 Ligands: ADP.16 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

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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