MolNFT v1 · #28908 · protein + RNA

Localization and dynamic behavior of ribosomal protein L30E

1YSH · RNA (28-mer): “Localization and dynamic behavior of ribosomal protein L30E”. Electron microscopy, 9 pockets (best druggability 0.72). MolNFT v1 #28908 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YSH
Type: protein + RNA
Length: 423 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (28-mer); RNA (34-mer); RNA (101-mer); Ribosomal protein L30; Ribosomal protein L37A…
UniProt: Q5I7K9, Q5QM99
Pockets: 9 · best druggability 0.72

Structure

electron microscopy · 6 distinct chains · 47% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (28-mer)	rna	28	—	—
F	RNA (34-mer)	rna	33	—	—
B	RNA (101-mer)	rna	101	—	—
C	Ribosomal protein L30	protein	104	37% helix, 13% strand	Q5I7K9
D	Ribosomal protein L37A	protein	73	37% helix, 18% strand	Q5QM99
E	40S ribosomal protein S13	protein	84	68% helix, 0% strand	—

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	585	0.72	0.80	64	empty
2	428	0.60	0.76	37	empty
3	340	0.56	0.76	35	empty
4	424	0.54	0.74	24	empty
5	384	0.52	0.73	35	empty

Interfaces

10 interfaces between chains.

B–E · 974 Å² buried · 34 hydrogen bonds · protein-nucleic
F–C · 502 Å² buried · 29 hydrogen bonds · protein-nucleic
A–E · 359 Å² buried · 33 hydrogen bonds · protein-nucleic
C–E · 353 Å² buried · 1 hydrogen bond · protein-protein
A–D · 275 Å² buried · 3 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide, 1 isopeptide (disulfide, isopeptide).

Compared structures

1YSH · Localization and dynamic behavior of ribosomal protein L30e · the same entry in another collection · chain B against B, TM-score 1.00
Q5I7K9 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L30 (Q5I7K9) · a predicted model of the same protein · chain C against A, TM-score 0.79

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 Q5I7K9
Every structure of UniProt Q5QM99
Elsewhere: RCSB PDB 1YSH · PDBe 1YSH · UniProt Q5I7K9 · UniProt Q5QM99

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