SMTL ID : 8q3q.1

Bacterial transcription termination factor Rho G152D mutant

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.159, A:P.182, A:K.184, A:A.185, A:G.186, A:K.187, A:T.188 Salt bridges: A:K.187 pi-Stacking: A:F.358, A:F.358 ADP.3: 14 residues within 4Å: Chain B: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain C: R.369, E.372 Ligands: MG.4 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:D.159, B:P.182, B:K.184, B:A.185, B:G.186, B:K.187, B:T.188, C:E.372 Salt bridges: B:K.187, C:R.369, C:R.369 pi-Stacking: B:F.358, B:F.358 ADP.5: 14 residues within 4Å: Chain C: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain D: R.369, E.372 Ligands: MG.6 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.159, C:P.182, C:K.184, C:A.185, C:G.186, C:K.187, C:T.188, D:E.372 Salt bridges: C:K.187, D:R.369, D:R.369 pi-Stacking: C:F.358, C:F.358 ADP.7: 14 residues within 4Å: Chain D: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain E: R.369, E.372 Ligands: MG.8 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:D.159, D:P.182, D:K.184, D:A.185, D:G.186, D:K.187, D:T.188, E:E.372 Salt bridges: D:K.187, E:R.369, E:R.369 pi-Stacking: D:F.358, D:F.358 ADP.9: 14 residues within 4Å: Chain E: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain F: R.369, E.372 Ligands: MG.10 13 PLIP interactions: 3 interactions with chain F, 10 interactions with chain E Hydrogen bonds: F:E.372, E:D.159, E:P.182, E:K.184, E:A.185, E:G.186, E:K.187, E:T.188 Salt bridges: F:R.369, F:R.369, E:K.187 pi-Stacking: E:F.358, E:F.358 ADP.11: 14 residues within 4Å: Chain F: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain G: R.369, E.372 Ligands: MG.12 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:D.159, F:P.182, F:K.184, F:A.185, F:G.186, F:K.187, F:T.188, G:E.372 Salt bridges: F:K.187, G:R.369, G:R.369 pi-Stacking: F:F.358 ADP.13: 14 residues within 4Å: Chain G: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain H: R.369, E.372 Ligands: MG.14 13 PLIP interactions: 3 interactions with chain H, 10 interactions with chain G Hydrogen bonds: H:E.372, G:D.159, G:P.182, G:K.184, G:A.185, G:G.186, G:K.187, G:T.188 Salt bridges: H:R.369, H:R.369, G:K.187 pi-Stacking: G:F.358, G:F.358 ADP.15: 14 residues within 4Å: Chain H: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain I: R.369, E.372 Ligands: MG.16 13 PLIP interactions: 10 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:D.159, H:P.182, H:K.184, H:A.185, H:G.186, H:K.187, H:T.188, I:E.372 Salt bridges: H:K.187, I:R.369, I:R.369 pi-Stacking: H:F.358, H:F.358 ADP.17: 14 residues within 4Å: Chain I: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain J: R.369, E.372 Ligands: MG.18 13 PLIP interactions: 10 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:D.159, I:P.182, I:K.184, I:A.185, I:G.186, I:K.187, I:T.188, J:E.372 Salt bridges: I:K.187, J:R.369, J:R.369 pi-Stacking: I:F.358, I:F.358 ADP.19: 14 residues within 4Å: Chain J: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain K: R.369, E.372 Ligands: MG.20 13 PLIP interactions: 10 interactions with chain J, 3 interactions with chain K Hydrogen bonds: J:D.159, J:P.182, J:K.184, J:A.185, J:G.186, J:K.187, J:T.188, K:E.372 Salt bridges: J:K.187, K:R.369, K:R.369 pi-Stacking: J:F.358, J:F.358 ADP.21: 14 residues within 4Å: Chain K: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain L: R.369, E.372 Ligands: MG.22 13 PLIP interactions: 10 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:D.159, K:P.182, K:K.184, K:A.185, K:G.186, K:K.187, K:T.188, L:E.372 Salt bridges: K:K.187, L:R.369, L:R.369 pi-Stacking: K:F.358, K:F.358 ADP.23: 14 residues within 4Å: Chain L: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain M: R.369, E.372 Ligands: MG.24 13 PLIP interactions: 3 interactions with chain M, 10 interactions with chain L Hydrogen bonds: M:E.372, L:D.159, L:P.182, L:K.184, L:A.185, L:G.186, L:K.187, L:T.188 Salt bridges: M:R.369, M:R.369, L:K.187 pi-Stacking: L:F.358, L:F.358 ADP.25: 14 residues within 4Å: Chain M: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain N: R.369, E.372 Ligands: MG.26 13 PLIP interactions: 3 interactions with chain N, 10 interactions with chain M Hydrogen bonds: N:E.372, M:D.159, M:P.182, M:K.184, M:A.185, M:G.186, M:K.187, M:T.188 Salt bridges: N:R.369, N:R.369, M:K.187 pi-Stacking: M:F.358, M:F.358 ADP.27: 14 residues within 4Å: Chain N: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain O: R.369, E.372 Ligands: MG.28 13 PLIP interactions: 10 interactions with chain N, 3 interactions with chain O Hydrogen bonds: N:D.159, N:P.182, N:K.184, N:A.185, N:G.186, N:K.187, N:T.188, O:E.372 Salt bridges: N:K.187, O:R.369, O:R.369 pi-Stacking: N:F.358, N:F.358 ADP.29: 14 residues within 4Å: Chain O: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain P: R.369, E.372 Ligands: MG.30 13 PLIP interactions: 10 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:D.159, O:P.182, O:K.184, O:A.185, O:G.186, O:K.187, O:T.188, P:E.372 Salt bridges: O:K.187, P:R.369, P:R.369 pi-Stacking: O:F.358, O:F.358 ADP.31: 14 residues within 4Å: Chain P: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain Q: R.369, E.372 Ligands: MG.32 13 PLIP interactions: 3 interactions with chain Q, 10 interactions with chain P Hydrogen bonds: Q:E.372, P:D.159, P:P.182, P:K.184, P:A.185, P:G.186, P:K.187, P:T.188 Salt bridges: Q:R.369, Q:R.369, P:K.187 pi-Stacking: P:F.358, P:F.358 ADP.33: 14 residues within 4Å: Chain Q: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Chain R: R.369, E.372 Ligands: MG.34 13 PLIP interactions: 10 interactions with chain Q, 3 interactions with chain R Hydrogen bonds: Q:D.159, Q:P.182, Q:K.184, Q:A.185, Q:G.186, Q:K.187, Q:T.188, R:E.372 Salt bridges: Q:K.187, R:R.369, R:R.369 pi-Stacking: Q:F.358, Q:F.358 ADP.35: 14 residues within 4Å: Chain A: R.369, E.372 Chain R: D.159, T.161, P.182, P.183, K.184, A.185, G.186, K.187, T.188, M.189, F.358 Ligands: MG.36 13 PLIP interactions: 10 interactions with chain R, 3 interactions with chain A Hydrogen bonds: R:D.159, R:P.182, R:K.184, R:A.185, R:G.186, R:K.187, R:T.188, A:E.372 Salt bridges: R:K.187, A:R.369, A:R.369 pi-Stacking: R:F.358, R:F.358

18 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: K.187, T.188 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: K.187, T.188 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: K.187, T.188 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: K.187, T.188 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: K.187, T.188 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain F: K.187, T.188 Chain G: R.369 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain G: K.187, T.188 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain H: K.187, T.188 Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain I: K.187, T.188 Chain J: R.369 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain J: K.187, T.188 Ligands: ADP.19 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain K: K.187, T.188 Ligands: ADP.21 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain L: K.187, T.188 Chain M: R.369 Ligands: ADP.23 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain M: K.187, T.188 Chain N: R.369 Ligands: ADP.25 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain N: K.187, T.188 Ligands: ADP.27 No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain O: K.187, T.188 Ligands: ADP.29 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain P: K.187, T.188 Chain Q: R.369 Ligands: ADP.31 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain Q: K.187, T.188 Ligands: ADP.33 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain R: K.187, T.188 Ligands: ADP.35 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Transcription termination factor rho polymerizes under stress. Biorxiv (2023)

Release Date

2023-09-27

Peptides

Transcription termination factor Rho: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
r

C
q

D
p

E
o

F
n

G
m

H
l

I
k

J
j

K
i

L
h

M
g

N
f

O
e

P
d

Q
c

R
b

Transcription termination factor Rho