GL1X · GenesisL1 explorer

MolNFT v2 · #128395 · protein + RNA

Hibernating ribosome from Staphylococcus aureus (Rotated state)

5ND9: “Hibernating ribosome from Staphylococcus aureus (Rotated state)”. Electron microscopy at 3.7. MolNFT v2 #128395 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5ND9
Type
protein + RNA
Length
10,030 residues
Chains
52
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.7
Source
Staphylococcus aureus (strain NCTC 8325); Staphylococcus aureus subsp. aureus…
UniProt
Q2FZ25, Q2FW12, Q2FXK6, Q2FW23, Q2G113, P48940, Q2FW20, Q2FW39, Q931G5, Q2FW31, P0A0H0, Q2FW30, Q2FW19, Q2G2Q1, Q2FZ45, Q2FW15, Q2G111, Q2FW10, Q2FXY6, Q2FXZ7, Q2G055, P60430, Q2FW06, Q2FW07, Q2FW18, Q2FW21, Q2FW38, Q2FW16, P0A0F8, Q2FW13, Q2FW33, Q2FW22, Q2FZ42, Q2FXQ1, Q2FXS8, Q2FW11, Q2FW08, Q2FW17, Q2G0S0, Q2FXT0, Q2FZ60, Q2FW14, P0A0G2, Q2FWD8, Q2FZF1, Q2FY22, Q2FUQ0, Q2FXQ0, Q2FW29

Structure

electron microscopy · resolution 3.7 · 52 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
a—rna1541——
b—protein222—Q2FZ25
c—protein203—Q2FW12
d—protein197—Q2FXK6
e—protein160—Q2FW23
f—protein94—Q2G113
g—protein143—P48940
h—protein131—Q2FW20
i—protein128—Q2FW39
j—protein99—Q931G5
k—protein115—Q2FW31
l—protein135—P0A0H0
m—protein110—Q2FW30
n—protein60—Q2FW19
o—protein88—Q2G2Q1
p—protein90—Q2FZ45
q—protein85—Q2FW15
r—protein56—Q2G111
s—protein84—Q2FW10
t—protein80—Q2FXY6
u—protein45—Q2FXZ7
v—protein101—Q2G055
A—rna2914——
B—rna114——
D—protein275—P60430
E—protein218—Q2FW06
F—protein199—Q2FW07
G—protein166—Q2FW18
H—protein164—Q2FW21
M—protein145—Q2FW38
N—protein122—Q2FW16
O—protein131—P0A0F8
P—protein133—Q2FW13
Q—protein117—Q2FW33
R—protein119—Q2FW22
S—protein107—Q2FZ42
T—protein116—Q2FXQ1
U—protein102—Q2FXS8
V—protein112—Q2FW11
W—protein89—Q2FW08
X—protein87—Q2FW17
Y—protein94—Q2G0S0
Z—protein77—Q2FXT0
0—protein46—Q2FZ60
1—protein65—Q2FW14
2—protein57—P0A0G2
3—protein81—Q2FWD8
4—protein44—Q2FZF1
5—protein28—Q2FY22
6—protein44—Q2FUQ0
7—protein60—Q2FXQ0
8—protein37—Q2FW29

Compared structures

  • Q2FW38 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (Q2FW38) · a predicted model of the same protein · chain M against A, TM-score 0.96
  • Q2FW07 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (Q2FW07) · a predicted model of the same protein · chain F against A, TM-score 0.95
  • Q2FW20 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (Q2FW20) · a predicted model of the same protein · chain h against A, TM-score 0.95
  • Q2FW33 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L17 (Q2FW33) · a predicted model of the same protein · chain Q against A, TM-score 0.94
  • Q2FW14 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L29 (Q2FW14) · a predicted model of the same protein · chain 1 against A, TM-score 0.92
  • Q2FZ45 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (Q2FZ45) · a predicted model of the same protein · chain p against A, TM-score 0.91
  • Q931G5 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S10 (Q931G5) · a predicted model of the same protein · chain j against A, TM-score 0.90
  • Q2FW08 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L23 (Q2FW08) · a predicted model of the same protein · chain W against A, TM-score 0.88
  • Q2FW39 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S9 (Q2FW39) · a predicted model of the same protein · chain i against A, TM-score 0.88
  • P0A0F8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L15 (P0A0F8) · a predicted model of the same protein · chain O against A, TM-score 0.83
  • Q2FXQ0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L35 (Q2FXQ0) · a predicted model of the same protein · chain 7 against A, TM-score 0.82
  • Q2G055 · AlphaFold monomer V2.0 prediction for ribosome hibernation promotion factor (Q2G055) · a predicted model of the same protein · chain v against A, TM-score 0.82

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