SMTL ID : 3ice.1

Rho transcription termination factor bound to RNA and ADP-BeF3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: P.183, 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: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.184, A:A.185, A:G.186, A:K.187, A:T.188, B:K.370 Water bridges: A:K.187, A:T.188, A:R.215, A:E.218, B:R.369 Salt bridges: A:K.187, B:R.369, B:R.369 pi-Stacking: A:F.358, A:F.358 ADP.4: 12 residues within 4Å: Chain B: P.183, 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 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:K.184, B:A.185, B:G.186, B:K.187, B:T.188, C:K.370 Water bridges: B:T.188, B:R.215, B:T.321, C:R.369 Salt bridges: B:K.187, C:R.369, C:R.369 pi-Stacking: B:F.358, B:F.358 ADP.7: 12 residues within 4Å: Chain C: P.183, 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: 11 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:K.184, C:A.185, C:G.186, C:K.187, C:T.188, C:T.188, D:R.369, D:K.370 Water bridges: C:R.215, C:R.215 Salt bridges: C:K.187, D:R.369, D:R.369 pi-Stacking: C:F.358, C:F.358 ADP.10: 12 residues within 4Å: Chain D: P.183, 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 14 PLIP interactions: 11 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:T.188, D:R.215 Salt bridges: D:K.187, E:R.369, E:R.369 pi-Stacking: D:F.358, D:F.358 ADP.13: 14 residues within 4Å: Chain E: P.183, K.184, A.185, G.186, K.187, T.188, M.189, E.214, R.356, F.358 Chain F: R.369, K.370 Ligands: MG.14, BEF.15 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:K.184, E:A.185, E:G.186, E:K.187, E:T.188, E:E.214, E:R.356, F:K.370, F:K.370, F:K.370 Water bridges: E:T.188, E:E.218 Salt bridges: E:K.187 pi-Stacking: E:F.358, E:F.358 ADP.17: 14 residues within 4Å: Chain A: R.369, K.370 Chain F: P.183, K.184, A.185, G.186, K.187, T.188, M.189, R.215, E.218, F.358 Ligands: MG.18, BEF.19 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:K.184, F:A.185, F:G.186, F:K.187, F:T.188, F:R.215, F:E.218, A:K.370 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: 6 residues within 4Å: Chain A: T.188, E.214, E.218, D.268 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, E.214, D.268 Ligands: ADP.4, BEF.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.188, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain C: T.188, R.215, E.218 Ligands: ADP.7, BEF.9 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.188, H2O.2, H2O.3 MG.11: 7 residues within 4Å: Chain D: K.187, T.188, E.214, R.215, D.268 Ligands: ADP.10, BEF.12 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.188, D:E.214, H2O.3 MG.14: 6 residues within 4Å: Chain E: K.187, T.188, E.214, R.215 Ligands: ADP.13, BEF.15 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.188, E:E.214, H2O.3, H2O.3 MG.18: 3 residues within 4Å: Chain F: T.188 Ligands: ADP.17, BEF.19 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.188

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

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

2 x SPD: SPERMIDINE(Non-covalent)

SPD.16: 5 residues within 4Å: Chain E: E.237, P.238, S.240, R.241, Q.244 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:P.238, E:R.241, E:R.241 Hydrogen bonds: E:E.237, E:S.240, E:R.241, E:R.241, E:Q.244 SPD.20: 4 residues within 4Å: Chain A: G.285 Chain C: G.285 Chain G: U.1, U.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.285, C:G.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomsen, N.D. et al., Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell(Cambridge,Mass.) (2009)

Release Date

2009-11-10

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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