MolNFT v1 · #108168 · protein + RNA

Crystal structure of a signal recognition particle alu domain in the elongation arrest conformation

4UYK · Signal recognition particle 9 kda protein: “Crystal structure of a signal recognition particle alu domain in the elongation arrest conformation”. X-ray diffraction, 6 pockets (best druggability 0.75). MolNFT v1 #108168 on GenesisL1…

PDB: 4UYK
Type: protein + RNA
Length: 306 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Signal recognition particle 9 kda protein; Signal recognition particle 14 kda protein…
UniProt: P49458, P37108
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Signal recognition particle 9 kda protein	protein	82	44% helix, 27% strand	P49458
B	Signal recognition particle 14 kda protein	protein	90	36% helix, 28% strand	P37108
R	Srp RNA	rna	134	—	—

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	969	0.75	0.78	51	empty
2	768	0.64	0.74	47	empty
3	126	0.39	0.75	16	empty
4	110	0.32	0.72	10	empty
5	70	0.27	0.73	10	empty

Interfaces

3 interfaces between chains.

A–B · 1636 Å² buried · 22 hydrogen bonds · protein-protein
B–R · 843 Å² buried · 21 hydrogen bonds · protein-nucleic
A–R · 498 Å² buried · 12 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 modified (engineered, nucleotide modification).

Compared structures

4UYK · Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest… · the same entry in another collection · chain A against A, TM-score 1.00
P37108 · AlphaFold monomer V2.0 prediction for signal recognition particle 14 kda protein (P37108) · a predicted model of the same protein · chain B against A, TM-score 0.96
P49458 · AlphaFold monomer V2.0 prediction for signal recognition particle 9 kda protein (P49458) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P49458
Every structure of UniProt P37108
Elsewhere: RCSB PDB 4UYK · PDBe 4UYK · UniProt P49458 · UniProt P37108

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