SMTL ID : 8pew.1

Rho-ATPgS-Psu complex III expanded

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-18-16-mer

Ligands

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

AGS.1: 14 residues within 4Å: Chain 2: A.172, M.175 Chain A: 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 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.158, A:T.158, A:K.181, A:K.181, A:K.181, A:A.182, A:G.183, A:K.184, A:T.185, B:R.366, B:R.366, B:E.369 Salt bridges: A:K.181, A:K.184, B:R.366 pi-Stacking: A:F.355 AGS.3: 14 residues within 4Å: Chain 0: A.172, M.175 Chain B: T.158, K.181, A.182, G.183, K.184, T.185, M.186, E.211, F.355 Chain C: R.366, E.369 Ligands: MG.4 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.158, B:T.158, B:K.181, B:A.182, B:G.183, B:K.184, B:T.185, B:T.185, B:M.186, B:E.211, C:R.366, C:E.369 Salt bridges: B:K.184 pi-Stacking: B:F.355 AGS.5: 12 residues within 4Å: Chain C: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain D: K.367, E.369 Chain Y: A.172 Ligands: MG.6 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.158, C:T.158, C:K.181, C:A.182, C:G.183, C:K.184, C:K.184, C:T.185, C:T.185, C:M.186, D:K.367 Salt bridges: C:K.184, D:K.367 pi-Stacking: C:F.355 AGS.7: 11 residues within 4Å: Chain D: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain E: R.366, E.369 Chain W: A.172 Ligands: MG.8 10 PLIP interactions: 8 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, E:R.366, E:E.369 Salt bridges: D:K.184 pi-Stacking: D:F.355 AGS.9: 15 residues within 4Å: Chain E: T.158, P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.212, L.320, F.355 Chain F: R.366, E.369 Chain U: M.175 Ligands: MG.10 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:T.158, E:T.158, E:K.181, E:A.182, E:G.183, E:K.184, E:T.185, E:T.185, E:M.186, E:R.212 pi-Stacking: E:F.355 Salt bridges: F:R.366, F:R.366 AGS.11: 13 residues within 4Å: Chain F: P.180, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain G: R.366, E.369 Chain S: A.172, M.175 Ligands: MG.12 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:K.181, F:K.181, F:A.182, F:G.183, F:K.184, F:T.185, F:T.185, G:R.366 Salt bridges: F:K.181, F:K.181, F:K.184 pi-Stacking: F:F.355 AGS.13: 12 residues within 4Å: Chain 4: A.172 Chain G: K.181, A.182, G.183, K.184, T.185, M.186, L.187, F.355 Chain H: R.366, E.369 Ligands: MG.14 13 PLIP interactions: 10 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:K.181, G:A.182, G:G.183, G:K.184, G:K.184, G:T.185, G:T.185, H:R.366, H:E.369 Salt bridges: G:K.181, G:K.184, H:R.366 pi-Stacking: G:F.355 AGS.15: 9 residues within 4Å: Chain H: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain Q: R.366 Ligands: MG.16 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain Q Hydrogen bonds: H:K.181, H:A.182, H:G.183, H:K.184, H:T.185, H:T.185, H:M.186, Q:R.366 Salt bridges: H:K.184 AGS.17: 15 residues within 4Å: Chain I: T.154, T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain J: R.366, E.369 Chain T: A.172, M.175 Ligands: MG.18 12 PLIP interactions: 10 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:T.154, I:T.154, I:K.181, I:K.181, I:A.182, I:G.183, I:K.184, I:T.185, I:T.185, J:R.366, J:E.369 Salt bridges: I:K.184 AGS.19: 13 residues within 4Å: Chain J: T.158, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain K: R.366 Chain V: A.172, M.175 Ligands: MG.20 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:T.158, J:K.181, J:A.182, J:G.183, J:K.184, J:T.185, J:T.185 Salt bridges: J:K.184 AGS.21: 14 residues within 4Å: Chain K: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain L: R.366, K.367, E.369 Chain X: A.172, M.175 Ligands: MG.22 14 PLIP interactions: 10 interactions with chain K, 4 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:T.185, L:R.366, L:K.367, L:E.369 Salt bridges: K:K.184, L:K.367 pi-Stacking: K:F.355 AGS.23: 13 residues within 4Å: Chain L: K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain M: R.366, E.369 Chain Z: A.172, M.175 Ligands: MG.24 14 PLIP interactions: 11 interactions with chain L, 3 interactions with chain M Hydrogen bonds: L:K.181, L:A.182, L:G.183, L:K.184, L:T.185, L:T.185, L:R.212, M:R.366, M:R.366, M:E.369 Salt bridges: L:K.181, L:K.181, L:K.184 pi-Stacking: L:F.355 AGS.25: 14 residues within 4Å: Chain 1: A.172, M.175 Chain M: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355, P.356 Chain N: R.366, E.369 Ligands: MG.26 9 PLIP interactions: 7 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:K.181, M:A.182, M:G.183, M:K.184, M:T.185, M:T.185, N:R.366, N:E.369 Salt bridges: M:K.184 AGS.27: 13 residues within 4Å: Chain 3: A.172 Chain N: T.158, P.180, K.181, A.182, G.183, K.184, T.185, M.186, F.355, P.356 Chain O: R.366 Ligands: MG.28 17 PLIP interactions: 3 interactions with chain O, 14 interactions with chain N Hydrogen bonds: O:R.366, N:T.158, N:K.181, N:K.181, N:A.182, N:G.183, N:K.184, N:K.184, N:T.185, N:T.185, N:M.186 Salt bridges: O:R.366, O:R.366, N:K.181, N:K.181, N:K.184 pi-Stacking: N:F.355 AGS.29: 13 residues within 4Å: Chain 7: A.172, M.175 Chain O: T.158, K.181, A.182, G.183, K.184, T.185, M.186, L.187, F.355, P.356 Ligands: MG.30 9 PLIP interactions: 8 interactions with chain O, 1 interactions with chain P Hydrogen bonds: O:T.158, O:K.181, O:A.182, O:G.183, O:K.184, O:T.185, O:T.185 Salt bridges: O:K.184, P:K.367 AGS.31: 10 residues within 4Å: Chain P: K.181, A.182, G.183, K.184, T.185, M.186, R.353, F.355 Chain R: R.366 Ligands: MG.32 14 PLIP interactions: 12 interactions with chain P, 2 interactions with chain R Hydrogen bonds: P:K.181, P:K.181, P:K.181, P:A.182, P:G.183, P:K.184, P:T.185, P:T.185, P:M.186, P:R.353, R:R.366, R:R.366 Salt bridges: P:K.181, P:K.184

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.185 Chain B: R.366 Ligands: AGS.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: 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: 2 residues within 4Å: Chain D: T.185 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.185 MG.10: 4 residues within 4Å: Chain E: T.185, E.215 Chain F: R.366 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: 3 residues within 4Å: Chain G: K.184, T.185 Ligands: AGS.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: AGS.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.185 MG.18: 2 residues within 4Å: Chain I: T.185 Ligands: AGS.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.185 MG.20: 2 residues within 4Å: Chain J: T.185 Ligands: AGS.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.185 MG.22: 3 residues within 4Å: Chain K: K.184, T.185 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 MG.26: 2 residues within 4Å: Chain M: T.185 Ligands: AGS.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.185 MG.28: 4 residues within 4Å: Chain N: K.184, T.185 Chain O: R.366 Ligands: AGS.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.185 MG.30: 3 residues within 4Å: Chain O: K.184, T.185 Ligands: AGS.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.185 MG.32: 2 residues within 4Å: Chain P: T.185 Ligands: AGS.31 1 PLIP interactions: 1 interactions with chain P Metal complexes: P: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: ABCDEFGHIJKLMNOPQR
Polarity suppression protein: STUVWXYZ01234567

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
X

R
Y

S
a

T
b

U
c

V
d

W
e

X
f

Y
g

Z
h

0
i

1
j

2
k

3
l

4
m

5
n

6
o

7
p

Transcription termination factor Rho

Polarity suppression protein

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