MolNFT v1 · #161636 · protein + RNA

Mechanism of EIF6 release from the nascent 60S ribosomal subunit

6QKL · 26S ribosomal RNA: “Mechanism of EIF6 release from the nascent 60S ribosomal subunit”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #161636 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QKL
Type: protein + RNA
Length: 3,024 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26S ribosomal RNA; 60S ribosomal protein L3; 60S ribosomal protein L9; 60S ribosomal…
UniProt: P34113, Q54XI5, Q54G86, Q54J69, Q54VN6, P14794, Q551M2, Q9Y3A5, P22685, Q54J50
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 11 distinct chains · 17% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N	26S ribosomal RNA	rna	1158	—	—
A	60S ribosomal protein L3	protein	388	10% helix, 24% strand	P34113
B	60S ribosomal protein L9	protein	185	17% helix, 32% strand	Q54XI5
E	60S ribosomal protein L23	protein	128	5% helix, 32% strand	Q54G86
F	60S ribosomal protein L10	protein	216	21% helix, 21% strand	Q54J69
G	60S ribosomal protein L24	protein	53	15% helix, 23% strand	Q54VN6
H	Ubiquitin-60S ribosomal protein L40	protein	51	22% helix, 12% strand	P14794
I	Eukaryotic translation initiation factor 6	protein	224	22% helix, 16% strand	Q551M2
J	Ribosome maturation protein sbds	protein	250	26% helix, 21% strand	Q9Y3A5
C	60S acidic ribosomal protein P0	protein	205	16% helix, 11% strand	P22685
D	60S ribosomal protein L12	protein	166	13% helix, 2% strand	Q54J50

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1160	0.84	0.86	93	empty
2	915	0.84	0.87	90	empty
3	734	0.84	0.88	73	empty
4	1004	0.83	0.85	75	empty
5	928	0.81	0.84	67	empty

Interfaces

23 interfaces between chains.

N–A · 5942 Å² buried · 114 hydrogen bonds · protein-nucleic
N–F · 3472 Å² buried · 59 hydrogen bonds · protein-nucleic
N–J · 2000 Å² buried · 30 hydrogen bonds · protein-nucleic
N–B · 1903 Å² buried · 31 hydrogen bonds · protein-nucleic
N–E · 1817 Å² buried · 34 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6QKL · Mechanism of eIF6 release from the nascent 60S ribosomal subunit · the same entry in another collection · chain D against D, TM-score 1.00
P34113 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3 (P34113) · a predicted model of the same protein · chain A 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 P34113
Every structure of UniProt Q54XI5
Every structure of UniProt Q54G86
Every structure of UniProt Q54J69
Every structure of UniProt Q54VN6
Every structure of UniProt P14794
Every structure of UniProt Q551M2
Every structure of UniProt Q9Y3A5
Every structure of UniProt P22685
Every structure of UniProt Q54J50
Elsewhere: RCSB PDB 6QKL · PDBe 6QKL · UniProt P34113 · UniProt Q54XI5 · UniProt Q54G86 · UniProt Q54J69 · UniProt Q54VN6 · UniProt P14794 · UniProt Q551M2 · UniProt Q9Y3A5 · UniProt P22685 · UniProt Q54J50

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