SMTL ID : 9gct.1

Rho-ATP-Psu complex II expanded

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-16-14-mer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: T.158, P.180, 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 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.158, A:T.158, A:K.181, 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:E.369 Salt bridges: A:K.181, A:K.184, A:K.184, A:R.212, B:R.366 pi-Stacking: A:F.355, A:F.355 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.368, E.369 Ligands: MG.4 15 PLIP interactions: 4 interactions with chain C, 11 interactions with chain B Hydrogen bonds: C:K.367, C:E.368, C:E.369, B:K.181, B:A.182, B:G.183, B:K.184, B:T.185, B:T.185, B:M.186, B:R.212 Salt bridges: C:R.366, B:K.184, B:K.184 pi-Stacking: B:F.355 ATP.5: 13 residues within 4Å: Chain C: T.158, K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain D: R.366, K.367, E.369 Chain W: A.172 Ligands: MG.6 15 PLIP interactions: 10 interactions with chain C, 5 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:T.185, D:K.367, D:K.367, D:E.369 Salt bridges: C:K.184, C:K.184, D:R.366, D:K.367 pi-Stacking: C:F.355 ATP.7: 15 residues within 4Å: Chain D: 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 Chain U: A.172, M.175 Ligands: MG.8 14 PLIP interactions: 4 interactions with chain E, 10 interactions with chain D Hydrogen bonds: E:K.367, E:E.369, D:K.181, D:A.182, D:G.183, D:K.184, D:T.185, D:M.186, D:E.215 Salt bridges: E:R.366, E:K.367, D:K.184, D:R.212 pi-Stacking: D:F.355 ATP.9: 11 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 S: A.172 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 Salt bridges: E:K.181, E:K.184, E:K.184, F:R.366, F:R.366 pi-Stacking: E:F.355 ATP.11: 11 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 Chain Q: A.172 Ligands: MG.12 12 PLIP interactions: 2 interactions with chain G, 10 interactions with chain F Salt bridges: G:R.366, G:K.367, F:K.181, F:K.184, F:K.184, F:R.212 Hydrogen bonds: F:K.181, F:A.182, F:G.183, F:K.184, F:T.185 pi-Stacking: F:F.355 ATP.13: 13 residues within 4Å: Chain G: P.180, K.181, A.182, G.183, K.184, T.185, M.186, L.187, R.353, F.355 Chain H: R.366, E.368 Ligands: MG.14 18 PLIP interactions: 14 interactions with chain G, 4 interactions with chain H Hydrogen bonds: G:K.181, G:A.182, G:G.183, G:K.184, G:T.185, G:R.353, G:R.353, H:E.368 Salt bridges: G:K.181, G:K.181, G:K.181, G:K.184, G:K.184, H:R.366, H:R.366, H:R.366 pi-Cation interactions: G:R.353, G:R.353 ATP.15: 9 residues within 4Å: Chain H: K.181, A.182, G.183, K.184, T.185, M.186, R.353, F.355 Ligands: MG.16 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:T.158, H:T.158, H:K.181, H:K.181, H:A.182, H:G.183, H:K.184, H:T.185, H:T.185, H:R.353, H:R.353 Salt bridges: H:K.181, H:K.184, H:K.184 pi-Stacking: H:F.355, H:F.355 ATP.17: 12 residues within 4Å: Chain I: T.158, P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.212, F.355 Chain J: R.366 Ligands: MG.18 11 PLIP interactions: 10 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:T.158, I:K.181, I:A.182, I:G.183, I:K.184, I:T.185, I:R.212 Salt bridges: I:K.184, I:K.184, J:R.366 pi-Stacking: I:F.355 ATP.19: 12 residues within 4Å: Chain J: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain K: R.366, K.367, E.369 Chain V: A.172 Ligands: MG.20 15 PLIP interactions: 10 interactions with chain J, 5 interactions with chain K Hydrogen bonds: J:K.181, J:A.182, J:G.183, J:K.184, J:T.185, J:M.186, K:K.367, K:K.367, K:E.369 Salt bridges: J:K.184, J:K.184, J:R.212, K:R.366, K:K.367 pi-Stacking: J:F.355 ATP.21: 12 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, E.369 Chain X: A.172 Ligands: MG.22 11 PLIP interactions: 9 interactions with chain K, 2 interactions with chain L Hydrogen bonds: K:K.181, K:A.182, K:G.183, K:K.184, K:T.185, K:R.212, L:E.369 Salt bridges: K:K.184, K:K.184, L:R.366 pi-Stacking: K:F.355 ATP.23: 11 residues within 4Å: Chain L: K.181, A.182, G.183, K.184, T.185, M.186, F.355 Chain M: R.366, E.369 Chain Z: A.172 Ligands: MG.24 10 PLIP interactions: 8 interactions with chain L, 2 interactions with chain M Hydrogen bonds: L:K.181, L:A.182, L:G.183, L:K.184, L:T.185, M:E.369 Salt bridges: L:K.184, L:K.184, M:R.366 pi-Stacking: L:F.355 ATP.25: 13 residues within 4Å: Chain 1: A.172 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 13 PLIP interactions: 11 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:T.158, M:K.181, M:A.182, M:G.183, M:K.184, M:T.185, M:M.186, N:E.369 Salt bridges: M:K.181, M:K.184, M:K.184, N:R.366 pi-Stacking: M:F.355 ATP.27: 13 residues within 4Å: Chain 3: A.172 Chain N: K.181, A.182, G.183, K.184, T.185, M.186, L.187, R.353, F.355, P.356 Chain O: R.366 Ligands: MG.28 13 PLIP interactions: 11 interactions with chain N, 2 interactions with chain O Hydrogen bonds: N:K.181, N:A.182, N:G.183, N:K.184, N:T.185, N:R.353, N:R.353 Salt bridges: N:K.181, N:K.184, N:K.184, O:R.366, O:K.367 pi-Stacking: N:F.355 ATP.29: 12 residues within 4Å: Chain O: P.180, K.181, A.182, G.183, K.184, T.185, M.186, R.353, F.355 Chain P: R.366, E.368 Ligands: MG.30 14 PLIP interactions: 11 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:K.181, O:A.182, O:G.183, O:K.184, O:T.185, O:T.185, O:R.353, O:R.353, P:E.368 Salt bridges: O:K.181, O:K.184, O:K.184, P:R.366, P:R.366

15 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.185, R.212 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: 3 residues within 4Å: Chain D: T.185, E.215 Ligands: ATP.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.215 Ligands: ATP.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: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.185 MG.14: 4 residues within 4Å: Chain G: K.184, T.185 Chain H: R.366 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 I: T.185 Ligands: ATP.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: ATP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.185 MG.22: 2 residues within 4Å: Chain K: T.185 Ligands: ATP.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: ATP.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: ATP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.185 MG.28: 3 residues within 4Å: Chain N: K.184, T.185 Ligands: ATP.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.185 MG.30: 3 residues within 4Å: Chain O: T.185 Chain P: R.366 Ligands: ATP.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O: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: ABCDEFGHIJKLMNOP
Polarity suppression protein: QRSTUVWXYZ0123

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
J

J
K

K
L

L
M

M
N

N
O

O
P

P
Y

Q
a

R
b

S
c

T
d

U
e

V
f

W
g

X
h

Y
i

Z
j

0
k

1
l

2
o

3
p

Transcription termination factor Rho

Polarity suppression protein

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