SMTL ID : 5jjl.1

Rho transcription termination factor bound to rU8 and 5 ADP-BeF3 molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: T.161, P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain B: R.369, K.370 Ligands: MG.2, BEF.3 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.161, A:K.184, A:A.185, A:G.186, A:K.187, A:T.188, B:K.370 Water bridges: A:T.188, B:R.369, B:R.369 Salt bridges: A:K.187, B:R.369, B:R.369 pi-Stacking: A:F.358, A:F.358 ADP.4: 13 residues within 4Å: Chain B: T.161, P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain C: R.369, K.370 Ligands: MG.5, BEF.6 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:T.161, B:K.184, B:A.185, B:G.186, B:K.187, B:T.188, C:K.370 Water bridges: B:T.188 Salt bridges: B:K.187, C:R.369, C:R.369 pi-Stacking: B:F.358, B:F.358 ADP.7: 13 residues within 4Å: Chain C: T.161, P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain D: R.369, K.370 Ligands: MG.8, BEF.9 15 PLIP interactions: 4 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:K.370, C:T.161, C:K.184, C:A.185, C:G.186, C:K.187, C:T.188, C:T.188 Water bridges: D:R.369, C:T.188 Salt bridges: D:R.369, D:R.369, C:K.187 pi-Stacking: C:F.358, C:F.358 ADP.10: 12 residues within 4Å: Chain D: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain E: R.369, K.370 Ligands: MG.11, BEF.12 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:K.184, D:A.185, D:G.186, D:K.187, D:T.188, D:T.188, E:K.370 Water bridges: D:K.187, D:T.188, D:R.215, D:R.215, D:R.215 Salt bridges: D:K.187, E:R.369, E:R.369 pi-Stacking: D:F.358, D:F.358 ADP.13: 13 residues within 4Å: Chain A: R.369, K.370, E.372 Chain F: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Ligands: MG.14, BEF.15 14 PLIP interactions: 10 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:K.184, F:A.185, F:G.186, F:K.187, F:T.188, A:K.370, A:E.372 Water bridges: F:T.188, F:T.188 Salt bridges: F:K.187, A:R.369, A:R.369 pi-Stacking: F:F.358, F:F.358

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.188, R.215 Ligands: ADP.1, BEF.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.188, H2O.1, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain B: T.188, R.215 Ligands: ADP.4, BEF.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.188, H2O.1, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain C: T.188, R.215 Ligands: ADP.7, BEF.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.188, H2O.1, H2O.1, H2O.1 MG.11: 5 residues within 4Å: Chain D: T.188, R.215, E.218 Ligands: ADP.10, BEF.12 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.188, H2O.1, H2O.1, H2O.1 MG.14: 3 residues within 4Å: Chain F: T.188 Ligands: ADP.13, BEF.15 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.188, H2O.1, H2O.1, H2O.1

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

BEF.3: 10 residues within 4Å: Chain A: P.183, K.184, K.187, R.215, L.323 Chain B: K.339, G.340, R.369 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.6: 10 residues within 4Å: Chain B: P.183, K.184, K.187, R.215, L.323 Chain C: K.339, G.340, R.369 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.9: 11 residues within 4Å: Chain C: P.183, K.184, K.187, T.188, R.215, L.323 Chain D: K.339, G.340, R.369 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.12: 10 residues within 4Å: Chain D: P.183, K.184, K.187, T.188, R.215, L.323 Chain E: G.340, R.369 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 8 residues within 4Å: Chain A: R.369 Chain F: P.183, K.184, K.187, R.215, L.323 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomsen, N.D. et al., Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-11-16

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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