SMTL ID : 9gcs.1

Rho-ATP-Psu complex II

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-10-mer

Ligands

12 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 12 residues within 4Å: Chain A: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain B: R.366, K.367, E.369 Chain M: A.172 Ligands: MG.2 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.182, A:G.183, A:K.184, A:T.185, B:K.367 Salt bridges: A:K.184, A:K.184, B:R.366 ATP.3: 13 residues within 4Å: Chain B: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain C: R.366, K.367, E.369 Chain K: A.172 Ligands: MG.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.181, B:A.182, B:G.183, B:K.184, B:T.185, B:T.185, B:M.186, C:K.367, C:E.369 Salt bridges: B:K.184, B:K.184, B:R.212, C:R.366 pi-Stacking: B:F.355 ATP.5: 13 residues within 4Å: Chain C: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain I: A.172 Chain V: R.366, K.367, E.369 Ligands: MG.6 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain V Hydrogen bonds: C:K.181, C:A.182, C:G.183, C:K.184, C:T.185, C:T.185, V:E.369 Salt bridges: C:K.184, C:K.184, C:R.212, V:R.366 pi-Stacking: C:F.355 ATP.7: 11 residues within 4Å: Chain D: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain E: R.366, K.367 Ligands: MG.8 14 PLIP interactions: 11 interactions with chain D, 3 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:R.212, E:K.367 Salt bridges: D:K.184, D:K.184, D:R.212, E:R.366, E:R.366 pi-Stacking: D:F.355 ATP.9: 13 residues within 4Å: Chain E: K.181, A.182, G.183, K.184, T.185, M.186, R.212, E.215, F.355 Chain F: R.366, K.367, E.369 Ligands: MG.10 14 PLIP interactions: 4 interactions with chain F, 10 interactions with chain E Hydrogen bonds: F:K.367, F:E.369, E:K.181, E:A.182, E:G.183, E:K.184, E:T.185, E:R.212 Salt bridges: F:R.366, F:K.367, E:K.184, E:K.184 pi-Stacking: E:F.355, E:F.355 ATP.11: 13 residues within 4Å: Chain F: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain G: R.366, K.367, E.369 Chain N: A.172 Ligands: MG.12 14 PLIP interactions: 10 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:K.181, F:A.182, F:G.183, F:K.184, F:T.185, F:M.186, G:K.367, G:E.369 Salt bridges: F:K.184, F:K.184, F:R.212, G:R.366, G:R.366 pi-Stacking: F:F.355 ATP.13: 11 residues within 4Å: Chain G: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain P: A.172 Chain U: R.366, E.369 Ligands: MG.14 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain U Hydrogen bonds: G:K.181, G:A.182, G:G.183, G:K.184, G:T.185, G:T.185, U:E.369 Salt bridges: G:K.184, G:K.184, U:R.366 pi-Stacking: G:F.355, G:F.355 ATP.15: 10 residues within 4Å: Chain H: K.181, A.182, G.183, K.184, T.185, M.186, L.187, R.353, F.355 Ligands: MG.16 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:K.181, H:A.182, H:G.183, H:K.184, H:T.185, H:T.185, H:T.185, H:R.269, H:F.355 Salt bridges: H:K.181, H:K.184, H:K.184 ATP.17: 10 residues within 4Å: Chain A: R.366 Chain S: K.181, A.182, G.183, K.184, T.185, M.186, F.355, P.356 Ligands: MG.18 13 PLIP interactions: 11 interactions with chain S, 2 interactions with chain A Hydrogen bonds: S:T.158, S:T.158, S:K.181, S:A.182, S:G.183, S:K.184, S:T.185, S:T.185 Salt bridges: S:K.184, S:K.184, A:R.366, A:R.366 pi-Stacking: S:F.355 ATP.19: 9 residues within 4Å: Chain S: R.366 Chain T: A.182, G.183, K.184, T.185, M.186, E.211, F.355 Ligands: MG.20 12 PLIP interactions: 9 interactions with chain T, 3 interactions with chain S Hydrogen bonds: T:A.182, T:G.183, T:K.184, T:T.185, T:M.186 Salt bridges: T:K.184, T:K.184, T:R.212, S:R.366, S:R.366, S:R.366 pi-Stacking: T:F.355 ATP.21: 11 residues within 4Å: Chain H: R.366 Chain R: A.172 Chain U: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Ligands: MG.22 11 PLIP interactions: 1 interactions with chain H, 10 interactions with chain U Salt bridges: H:R.366, U:K.184, U:K.184 Hydrogen bonds: U:T.158, U:K.181, U:A.182, U:G.183, U:K.184, U:T.185 pi-Stacking: U:F.355, U:F.355 ATP.23: 10 residues within 4Å: Chain V: K.181, A.182, G.183, K.184, T.185, M.186, R.212, R.353, F.355 Ligands: MG.24 14 PLIP interactions: 14 interactions with chain V Hydrogen bonds: V:K.181, V:A.182, V:G.183, V:K.184, V:T.185, V:T.185, V:E.215 Salt bridges: V:K.181, V:K.181, V:K.184, V:K.184, V:R.212 pi-Stacking: V:F.355 pi-Cation interactions: V:R.353

12 x MG: MAGNESIUM ION(Non-covalent)

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

2024-10-09

Peptides

Transcription termination factor Rho: ABCDEFGHSTUV
Polarity suppression protein: IJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
J

E
K

F
L

G
M

H
O

S
B

T
G

U
N

V
F

I
c

J
d

K
e

L
f

M
g

N
h

O
i

P
j

Q
k

R
l

Transcription termination factor Rho

Polarity suppression protein

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