MolNFT v1 · #53864 · protein + RNA

Mechanism of EIF6S anti-association activity

2X7N · Sarcin-ricin loop: “Mechanism of EIF6S anti-association activity”. Electron microscopy, 5 pockets (best druggability 0.80). MolNFT v1 #53864 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2X7N
Type: protein + RNA
Length: 440 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sarcin-ricin loop; Eukaryotic translation initiation factor 6; 60S ribosomal protein L23…
UniProt: Q12522, P04451, P04449
Pockets: 5 · best druggability 0.80

Structure

electron microscopy · 4 distinct chains · 22% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sarcin-ricin loop	rna	28	—	—
B	Eukaryotic translation initiation factor 6	protein	224	32% helix, 28% strand	Q12522
C	60S ribosomal protein L23	protein	132	8% helix, 38% strand	P04451
D	60S ribosomal protein L24-a	protein	56	16% helix, 18% strand	P04449

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	123	0.80	0.98	31	empty
2	493	0.66	0.78	59	empty
3	329	0.56	0.76	39	empty
4	158	0.55	0.82	24	empty
5	161	0.49	0.77	23	empty

Interfaces

5 interfaces between chains.

B–C · 824 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 375 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 321 Å² buried · 13 hydrogen bonds · protein-nucleic
A–B · 253 Å² buried · 3 hydrogen bonds · protein-nucleic
C–D · 209 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2X7N · Mechanism of eIF6s anti-association activity · the same entry in another collection · chain A against A, TM-score 1.00
Q12522 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 6 (Q12522) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q12522
Every structure of UniProt P04451
Every structure of UniProt P04449
Elsewhere: RCSB PDB 2X7N · PDBe 2X7N · UniProt Q12522 · UniProt P04451 · UniProt P04449

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