SMTL ID : 5jji.1

Rho transcription termination factor bound to rU7 and 6 ADP-BeF3 molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 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 16 PLIP interactions: 9 interactions with chain A, 7 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 Salt bridges: A:K.187, B:R.369, B:R.369 pi-Stacking: A:F.358, A:F.358 Water bridges: B:R.369, B:R.369, B:K.370, B:K.370 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 16 PLIP interactions: 6 interactions with chain C, 10 interactions with chain B Hydrogen bonds: C:K.370, B:T.161, B:K.184, B:A.185, B:G.186, B:K.187, B:T.188 Water bridges: C:R.369, C:K.370, C:E.372, B:T.188 Salt bridges: C:R.369, C:R.369, B:K.187 pi-Stacking: B:F.358, B:F.358 ADP.8: 12 residues within 4Å: Chain C: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain D: R.369, K.370 Ligands: MG.9, BEF.10 16 PLIP interactions: 6 interactions with chain D, 10 interactions with chain C Hydrogen bonds: D:K.370, C:K.184, C:A.185, C:G.186, C:K.187, C:T.188 Water bridges: D:R.369, D:E.372, D:E.372, C:T.188, C:T.188 Salt bridges: D:R.369, D:R.369, C:K.187 pi-Stacking: C:F.358, C:F.358 ADP.11: 13 residues within 4Å: Chain D: T.161, P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain E: R.369, K.370 Ligands: MG.12, BEF.13 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:T.161, D:T.161, D:K.184, D:A.185, D:G.186, D:K.187, D:T.188, E:K.370 Water bridges: D:K.187, D:K.187, D:T.188, E:R.369 Salt bridges: D:K.187, E:R.369, E:R.369 pi-Stacking: D:F.358, D:F.358 ADP.14: 12 residues within 4Å: Chain E: T.161, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain F: R.369 Ligands: MG.15, BEF.16 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:P.182, E:K.184, E:A.185, E:G.186, E:K.187, E:T.188, F:R.369 Water bridges: E:R.215, E:R.215 Salt bridges: E:K.187 pi-Stacking: E:F.358, E:F.358 ADP.17: 15 residues within 4Å: Chain A: T.368, R.369, K.370, E.372 Chain F: T.161, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Ligands: MG.18, BEF.19 15 PLIP interactions: 11 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:T.161, F:T.161, 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 Salt bridges: F:K.187, A:R.369, A:R.369 pi-Stacking: F:F.358, F:F.358

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.188, R.215, E.218 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: 5 residues within 4Å: Chain B: T.188, R.215, E.218 Ligands: ADP.4, BEF.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.188, H2O.2, H2O.2, H2O.3 MG.9: 6 residues within 4Å: Chain C: T.188, R.215, E.218, D.268 Ligands: ADP.8, BEF.10 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.188, H2O.5, H2O.5, H2O.6 MG.12: 4 residues within 4Å: Chain D: T.188, R.215 Ligands: ADP.11, BEF.13 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.188, H2O.7, H2O.8, H2O.8 MG.15: 4 residues within 4Å: Chain E: T.188, E.218 Ligands: ADP.14, BEF.16 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.188, H2O.9, H2O.9, H2O.9 MG.18: 3 residues within 4Å: Chain F: T.188 Ligands: ADP.17, BEF.19 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.188, H2O.9, H2O.10, H2O.10

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

BEF.3: 10 residues within 4Å: Chain A: P.183, K.184, K.187, T.188, R.215, L.323 Chain B: G.340, R.369 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.6: 11 residues within 4Å: Chain B: P.183, K.184, K.187, T.188, R.215, L.323 Chain C: K.339, G.340, R.369 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.10: 11 residues within 4Å: Chain C: P.183, K.184, K.187, T.188, E.214, R.215, L.323 Chain D: G.340, R.369 Ligands: ADP.8, MG.9 No protein-ligand interaction detected (PLIP) BEF.13: 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.11, MG.12 No protein-ligand interaction detected (PLIP) BEF.16: 10 residues within 4Å: Chain E: P.183, K.184, K.187, T.188, R.215, R.272, L.323 Chain F: R.369 Ligands: ADP.14, MG.15 No protein-ligand interaction detected (PLIP) BEF.19: 10 residues within 4Å: Chain A: R.369 Chain F: P.183, K.184, K.187, T.188, E.214, R.215, L.323 Ligands: ADP.17, MG.18 No protein-ligand interaction detected (PLIP)

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 7 residues within 4Å: Chain B: N.145, R.173, D.262, N.309, V.310, G.313, G.314 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.310, B:V.310

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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