SMTL ID : 6duq.1 (1 other biounit)

Structure of a Rho-NusG KOW domain complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-6-6-mer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain E: R.369, K.370 Ligands: MG.2, BEF.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:K.184, A:A.185, A:G.186, A:K.187, A:T.188, A:M.189, E:K.370 Salt bridges: A:K.187, E:R.369, E:R.369 pi-Stacking: A:F.358, A:F.358 ADP.4: 12 residues within 4Å: Chain A: R.369, K.370 Chain B: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Ligands: MG.5, BEF.6 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.184, B:A.185, B:G.186, B:K.187, B:T.188, B:M.189, A:K.370 Salt bridges: B:K.187, A:R.369, A:R.369 pi-Stacking: B:F.358, B:F.358 ADP.7: 12 residues within 4Å: Chain B: R.369, K.370 Chain C: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Ligands: MG.8, BEF.9 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.184, C:A.185, C:G.186, C:K.187, C:T.188, C:M.189, B:K.370 Salt bridges: C:K.187, B:R.369, B:R.369 pi-Stacking: C:F.358, C:F.358 ADP.10: 12 residues within 4Å: Chain C: R.369, K.370 Chain D: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Ligands: MG.11, BEF.12 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:K.370, C:E.372, D:K.184, D:A.185, D:G.186, D:K.187, D:T.188, D:M.189 Salt bridges: C:R.369, C:R.369, D:K.187 pi-Stacking: D:F.358, D:F.358 ADP.13: 12 residues within 4Å: Chain E: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain F: R.369, K.370 Ligands: MG.14, BEF.15 12 PLIP interactions: 3 interactions with chain F, 9 interactions with chain E Hydrogen bonds: F:R.369, F:K.370, E:K.184, E:A.185, E:G.186, E:K.187, E:T.188, E:M.189 Salt bridges: F:R.369, E:K.187 pi-Stacking: E:F.358, E:F.358 ADP.16: 12 residues within 4Å: Chain D: R.369, K.370 Chain F: P.182, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Ligands: MG.17, BEF.18 13 PLIP interactions: 4 interactions with chain D, 9 interactions with chain F Hydrogen bonds: D:K.370, D:E.372, F:K.184, F:A.185, F:G.186, F:K.187, F:T.188, F:M.189 Salt bridges: D:R.369, D:R.369, F:K.187 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, R.215, E.218, D.268 Ligands: ADP.1, BEF.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.188 MG.5: 5 residues within 4Å: Chain B: T.188, R.215, D.268 Ligands: ADP.4, BEF.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.188 MG.8: 6 residues within 4Å: Chain C: T.188, R.215, E.218, D.268 Ligands: ADP.7, BEF.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.188 MG.11: 6 residues within 4Å: Chain D: T.188, R.215, E.218, D.268 Ligands: ADP.10, BEF.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.188 MG.14: 6 residues within 4Å: Chain E: T.188, R.215, E.218, D.268 Ligands: ADP.13, BEF.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.188 MG.17: 5 residues within 4Å: Chain F: T.188, R.215, D.268 Ligands: ADP.16, BEF.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.188

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

BEF.3: 10 residues within 4Å: Chain A: P.183, K.184, K.187, T.188, E.214, R.215, L.323 Chain E: R.369 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.6: 11 residues within 4Å: Chain A: G.340, R.369 Chain B: P.183, K.184, K.187, T.188, E.214, R.215, L.323 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.9: 11 residues within 4Å: Chain B: G.340, R.369 Chain C: P.183, K.184, K.187, T.188, E.214, R.215, L.323 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.12: 10 residues within 4Å: Chain C: R.369 Chain D: P.183, K.184, K.187, T.188, E.214, R.215, L.323 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 10 residues within 4Å: Chain E: P.183, K.184, K.187, T.188, E.214, R.215, L.323 Chain F: R.369 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) BEF.18: 10 residues within 4Å: Chain D: R.369 Chain F: P.183, K.184, K.187, T.188, E.214, R.215, L.323 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lawson, M.R. et al., Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein. Mol. Cell (2018)

Release Date

2018-09-05

Peptides

Transcription termination factor Rho: ABCDEF
Transcription termination/antitermination protein NusG: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
G

C
H

D
I

E
K

F
J

G
P

H
Q

I
R

J
V

K
W

L
X

Transcription termination factor Rho

Transcription termination/antitermination protein NusG

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