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Structure of the human SRP68-RBD

Analyse Structure of the human SRP68-RBD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P3F
Type: protein
Length: 391 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.699
Source: Homo sapiens
Molecule: Signal recognition particle subunit SRP68
UniProt: Q9UHB9
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · resolution 1.699 · 2 distinct chains · 76% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Signal recognition particle subunit SRP68	protein	193	76% helix, 1% strand	Q9UHB9
B	Signal recognition particle subunit SRP68	protein	198	76% helix, 2% strand	Q9UHB9

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	667	0.80	0.85	63	empty
2	250	0.67	0.84	34	empty
3	75	0.32	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 899 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4P3F · Structure of the human SRP68-rbd · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHB9 · AlphaFold monomer V2.0 prediction for signal recognition particle subunit SRP68 (Q9UHB9) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 Q9UHB9
Elsewhere: RCSB PDB 4P3F · PDBe 4P3F · UniProt Q9UHB9

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