Research workbench

Crystal structure analysis of the translation factor RF3

Analyse Crystal structure analysis of the translation factor RF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VR1
Type: protein
Length: 2,064 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide chain release factor 3
UniProt: B8DIL5
Ligands: G4P
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Peptide chain release factor 3	protein	516	34% helix, 28% strand	B8DIL5

Ligands and binding sites

G4P · Guanosine-5',3'-tetraphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.80	0.82	122	empty
2	1072	0.79	0.81	107	G4P
3	586	0.78	0.84	64	G4P
4	672	0.77	0.83	63	G4P
5	628	0.76	0.82	62	G4P

Interfaces

4 interfaces between chains.

A–C · 1041 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1023 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 985 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 737 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3VR1 · Crystal structure analysis of the translation factor RF3 · the same entry in another collection · chain C against C, TM-score 1.00
B8DIL5 · AlphaFold monomer V2.0 prediction for peptide chain release factor 3 (B8DIL5) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 B8DIL5
Elsewhere: RCSB PDB 3VR1 · PDBe 3VR1 · UniProt B8DIL5

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