MolNFT v1 · #82556 · protein

Crystal structure analysis of the translation factor RF3

3VQT · Peptide chain release factor 3: “Crystal structure analysis of the translation factor RF3”. X-ray diffraction, 1 ligand (GDP), 20 pockets (best druggability 0.69). MolNFT v1 #82556 on GenesisL1: 3D structure, binding sites and…

PDB: 3VQT
Type: protein
Length: 1,970 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide chain release factor 3
UniProt: B8DIL5
Ligands: GDP
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide chain release factor 3	protein	495	32% helix, 30% strand	B8DIL5
B	Peptide chain release factor 3	protein	490	33% helix, 30% strand	B8DIL5
C	Peptide chain release factor 3	protein	491	32% helix, 30% strand	B8DIL5
D	Peptide chain release factor 3	protein	494	31% helix, 31% strand	B8DIL5

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	387	0.69	0.81	56	empty
2	314	0.67	0.82	41	empty
3	309	0.67	0.82	43	empty
4	87	0.65	0.91	19	empty
5	513	0.64	0.76	43	empty

Interfaces

3 interfaces between chains.

A–B · 1071 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1025 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 36 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3VQT · Crystal structure analysis of the translation factor RF3 · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.81

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 3VQT · PDBe 3VQT · UniProt B8DIL5

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