SMTL ID : 8peu.1

Rho-ATPgS-Psu complex III

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-mer

Ligands

10 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 13 residues within 4Å: Chain A: T.154, T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain B: R.366, E.369 Ligands: MG.2 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.158, A:T.158, A:K.181, A:A.182, A:G.183, A:K.184, A:T.185, A:T.185, A:R.212, B:R.366, B:R.366 Salt bridges: A:K.184, B:K.367 pi-Stacking: A:F.355 AGS.3: 13 residues within 4Å: Chain B: T.158, P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain C: R.366, E.369 Ligands: MG.4 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain B Hydrogen bonds: C:R.366, C:R.366, C:E.369, B:T.158, B:T.158, B:K.181, B:K.181, B:K.181, B:A.182, B:G.183, B:K.184, B:K.184, B:T.185, B:R.212 Salt bridges: C:K.367, B:K.184 pi-Stacking: B:F.355 AGS.5: 11 residues within 4Å: Chain C: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain D: R.366, E.369 Ligands: MG.6 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.181, C:K.181, C:A.182, C:G.183, C:K.184, C:K.184, C:T.185, C:T.185, C:M.186, C:R.212, D:R.366, D:E.369 Salt bridges: C:K.181, C:K.181, C:K.184 pi-Stacking: C:F.355, C:F.355 AGS.7: 13 residues within 4Å: Chain D: P.180, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain E: R.366, K.367, E.369 Chain O: A.172 Ligands: MG.8 11 PLIP interactions: 3 interactions with chain E, 8 interactions with chain D Salt bridges: E:R.366, E:R.366, E:K.367, D:K.184 Hydrogen bonds: D:K.181, D:A.182, D:G.183, D:T.185, D:T.185, D:M.186 pi-Stacking: D:F.355 AGS.9: 12 residues within 4Å: Chain E: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain F: R.366, E.369 Chain M: A.172, M.175 Ligands: MG.10 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:K.181, E:A.182, E:G.183, E:K.184, E:T.185, E:T.185, E:M.186, F:R.366, F:E.369 Salt bridges: E:K.184 pi-Stacking: E:F.355 AGS.11: 13 residues within 4Å: Chain G: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain H: R.366, K.367, E.369 Chain P: A.172 Ligands: MG.12 11 PLIP interactions: 2 interactions with chain H, 9 interactions with chain G Hydrogen bonds: H:R.366, G:K.181, G:K.181, G:A.182, G:G.183, G:K.184, G:T.185, G:T.185, G:M.186 Salt bridges: H:K.367, G:K.184 AGS.13: 12 residues within 4Å: Chain H: K.181, G.183, K.184, T.185, M.186, R.212, F.355 Chain I: R.366, K.367, E.369 Chain R: A.172 Ligands: MG.14 12 PLIP interactions: 4 interactions with chain I, 8 interactions with chain H Hydrogen bonds: I:R.366, I:E.368, I:E.369, H:K.181, H:G.183, H:K.184, H:T.185, H:T.185, H:R.212 Salt bridges: I:K.367, H:K.184 pi-Stacking: H:F.355 AGS.15: 13 residues within 4Å: Chain I: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain J: R.366, K.367, E.368, E.369 Chain T: A.172 Ligands: MG.16 15 PLIP interactions: 11 interactions with chain I, 4 interactions with chain J Hydrogen bonds: I:K.181, I:K.181, I:A.182, I:G.183, I:K.184, I:K.184, I:T.185, I:T.185, I:T.185, I:R.212, J:R.366, J:K.367, J:E.368 Salt bridges: I:K.184, J:K.367 AGS.17: 13 residues within 4Å: Chain J: P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain K: R.366, E.369 Chain V: M.175 Ligands: MG.18 11 PLIP interactions: 2 interactions with chain K, 9 interactions with chain J Hydrogen bonds: K:R.366, K:E.369, J:K.181, J:A.182, J:G.183, J:K.184, J:T.185, J:R.212, J:R.212 Salt bridges: J:K.184 pi-Stacking: J:F.355 AGS.19: 13 residues within 4Å: Chain K: T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain L: K.367, E.369 Chain X: A.172 Ligands: MG.20 11 PLIP interactions: 10 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:T.158, K:K.181, K:A.182, K:G.183, K:K.184, K:K.184, K:T.185, K:R.212 Salt bridges: K:K.184, L:K.367 pi-Stacking: K:F.355

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.185 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.185 MG.4: 3 residues within 4Å: Chain B: K.184, T.185 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.185 MG.6: 2 residues within 4Å: Chain C: T.185 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.185 MG.8: 3 residues within 4Å: Chain D: T.185 Chain E: R.366 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.185 MG.10: 3 residues within 4Å: Chain E: K.184, T.185 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.185 MG.12: 3 residues within 4Å: Chain G: K.184, T.185 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.185 MG.14: 3 residues within 4Å: Chain H: K.184, T.185 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.185 MG.16: 4 residues within 4Å: Chain I: K.184, T.185, R.212 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.185 MG.18: 3 residues within 4Å: Chain J: T.185, E.215 Ligands: AGS.17 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.185 MG.20: 3 residues within 4Å: Chain K: K.184, T.185 Ligands: AGS.19 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gjorgjevikj, D. et al., The Psu protein of phage satellite P4 inhibits transcription termination factor rho by forced hyper-oligomerization. Nat Commun (2025)

Release Date

2024-06-26

Peptides

Transcription termination factor Rho: ABCDEFGHIJKL
Polarity suppression protein: MNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
I

H
J

I
K

J
L

K
M

L
N

M
a

N
b

O
c

P
d

Q
e

R
f

S
g

T
h

U
i

V
j

W
k

X
l

Transcription termination factor Rho

Polarity suppression protein

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