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Structure of U2AF65 variant with BRU3 DNA

Analyse Structure of U2AF65 variant with BRU3 DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VAF
Type: protein + DNA
Length: 358 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Splicing factor U2AF 65 kda subunit; DNA 5'-D(*UP*UP*(BRU)P*(BRU)P*UP*UP*U)-3'
UniProt: P26368
Ligands: CPQ, SO4
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Splicing factor U2AF 65 kda subunit	protein	174	24% helix, 32% strand	P26368
B	Splicing factor U2AF 65 kda subunit	protein	172	28% helix, 31% strand	P26368
P, E	DNA 5'-D(UPUP(BRU)P(BRU)PUPUP*U)-3'	dna	6	—	—

Ligands and binding sites

CPQ · N,N-bis(3-D-gluconamidopropyl)deoxycholamide · ligand · chains B
SO4 · Sulfate ion · ion · 6 copies · chains A, B, E, P
DIO · 1,4-diethylene dioxide · additive · 4 copies · chains A, B
GOL · Glycerol · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	132	0.49	0.79	29	empty
2	151	0.39	0.73	24	SO4
3	89	0.37	0.76	22	empty

Interfaces

4 interfaces between chains.

B–E · 594 Å² buried · 18 hydrogen bonds · protein-nucleic
A–P · 565 Å² buried · 17 hydrogen bonds · protein-nucleic
B–P · 466 Å² buried · 8 hydrogen bonds · protein-nucleic
A–B · 290 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

3VAF · Structure of U2AF65 variant with BrU3 DNA · the same entry in another collection · chain A against A, TM-score 1.00
P26368 · AlphaFold monomer V2.0 prediction for splicing factor U2AF 65 kda subunit (P26368) · a predicted model of the same protein · chain A against A, TM-score 0.54

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 P26368
Elsewhere: RCSB PDB 3VAF · PDBe 3VAF · UniProt P26368

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