SMTL ID : 8pex.1

Rho P167L-ATPgS-Psu complex II

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-10-mer

Ligands

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

AGS.1: 16 residues within 4Å: Chain A: E.155, T.158, K.181, A.182, G.183, K.184, T.185, M.186, E.211, R.212, E.215, F.355 Chain B: R.366, K.367, E.369 Ligands: MG.2 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.155, A:T.158, A:K.181, A:A.182, A:G.183, A:K.184, A:T.185, A:T.185, A:M.186, A:R.212, A:R.212, B:R.366, B:R.366 Salt bridges: A:K.184, B:K.367 pi-Stacking: A:F.355 AGS.3: 14 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, K.367, E.369 Ligands: MG.4 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:R.366, C:E.369, B:T.158, B:T.158, B:K.181, B:A.182, B:G.183, B:K.184, B:T.185, B:M.186, B:R.212, B:R.212 Salt bridges: C:K.367, B:K.184 pi-Stacking: B:F.355 AGS.5: 13 residues within 4Å: Chain C: E.155, T.158, P.180, K.181, G.183, K.184, T.185, M.186, R.212, F.355 Chain D: R.366, E.369 Ligands: MG.6 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.155, C:T.158, C:K.181, C:A.182, C:G.183, C:K.184, C:T.185, C:M.186, C:R.212, D:R.366, D:E.369 Salt bridges: C:K.184 pi-Stacking: C:F.355 AGS.7: 14 residues within 4Å: Chain D: T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.212, E.215, F.355 Chain E: R.366, K.367, E.369 Ligands: MG.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:K.181, D:A.182, D:G.183, D:K.184, D:T.185, D:T.185, D:M.186, D:R.212, D:R.212, E:R.366 Salt bridges: D:K.184, E:K.367 pi-Stacking: D:F.355 AGS.9: 10 residues within 4Å: Chain E: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain F: R.366 Ligands: MG.10 10 PLIP interactions: 9 interactions with chain E, 1 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 Salt bridges: E:K.184 pi-Stacking: E:F.355 AGS.11: 9 residues within 4Å: Chain F: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.12 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:T.158, F:T.158, F:K.181, F:K.181, F:A.182, F:G.183, F:K.184, F:T.185, F:T.185, F:M.186 Salt bridges: F:K.181, F:K.181, F:K.184 pi-Stacking: F:F.355 AGS.13: 13 residues within 4Å: Chain G: T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain H: R.366, K.367, E.369 Ligands: MG.14 13 PLIP interactions: 10 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:T.158, G:K.181, G:A.182, G:G.183, G:K.184, G:T.185, G:T.185, G:M.186, G:R.212, H:R.366, H:E.369 pi-Stacking: G:F.355 Salt bridges: H:K.367 AGS.15: 14 residues within 4Å: Chain H: E.155, P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain I: R.366, E.369 Chain P: A.172 Ligands: MG.16 16 PLIP interactions: 13 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:E.155, H:K.181, H:A.182, H:G.183, H:K.184, H:T.185, H:T.185, H:T.185, H:M.186, H:R.212, H:R.212, I:R.366, I:E.369 Salt bridges: H:K.184, I:K.367 pi-Stacking: H:F.355 AGS.17: 14 residues within 4Å: Chain I: T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.212, E.215, F.355 Chain J: R.366, K.367, E.369 Ligands: MG.18 16 PLIP interactions: 11 interactions with chain I, 5 interactions with chain J Hydrogen bonds: I:K.181, I:A.182, I:G.183, I:K.184, I:T.185, I:T.185, I:M.186, I:R.212, I:R.212, J:R.366, J:R.366, J:K.367, J:K.367 Salt bridges: I:K.184, J:K.367 pi-Stacking: I:F.355 AGS.19: 12 residues within 4Å: Chain J: P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain T: A.172, M.175 Ligands: MG.20 12 PLIP interactions: 10 interactions with chain J, 2 interactions with chain K Hydrogen bonds: J:K.181, J:A.182, J:G.183, J:K.184, J:T.185, J:M.186, J:R.212, J:R.212, K:E.368 Salt bridges: J:K.184, K:K.367 pi-Stacking: J:F.355 AGS.21: 10 residues within 4Å: Chain K: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain L: R.366 Ligands: MG.22 10 PLIP interactions: 9 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:K.181, K:A.182, K:G.183, K:K.184, K:K.184, K:T.185, K:R.212, L:R.366 Salt bridges: K:K.184 pi-Stacking: K:F.355 AGS.23: 9 residues within 4Å: Chain L: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.24 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:T.158, L:K.181, L:K.181, L:K.181, L:A.182, L:G.183, L:K.184, L:K.184, L:T.185, L:T.185, L:M.186 Salt bridges: L:K.181, L:K.184 pi-Stacking: L:F.355

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.185, E.211, E.215 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.185 MG.4: 3 residues within 4Å: Chain B: T.185, E.211 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.185 MG.6: 3 residues within 4Å: Chain C: T.185, E.211 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.185 MG.8: 4 residues within 4Å: Chain D: T.185, E.211, E.215 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.185 MG.10: 3 residues within 4Å: Chain E: T.185, E.211 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.185 MG.12: 2 residues within 4Å: Chain F: T.185 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.185 MG.14: 2 residues within 4Å: Chain G: T.185 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.185 MG.16: 3 residues within 4Å: Chain H: T.185, E.211 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.185 MG.18: 3 residues within 4Å: Chain I: T.185, E.211 Ligands: AGS.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.185 MG.20: 3 residues within 4Å: Chain J: T.185, E.211 Ligands: AGS.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.185 MG.22: 3 residues within 4Å: Chain K: T.185, E.215 Ligands: AGS.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.185 MG.24: 3 residues within 4Å: Chain L: K.184, T.185 Ligands: AGS.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L: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: MNOPQRSTUV

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

Transcription termination factor Rho

Polarity suppression protein

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