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Structure of U2AF65 variant with BRU5C6 DNA

Analyse Structure of U2AF65 variant with BRU5C6 DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VAJ
Type: protein + DNA
Length: 362 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*UP*UP*(BRU)P*CP*U)-3')
UniProt: P26368
Ligands: CPQ, SO4
Pockets: 3 · best druggability 0.42

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Splicing factor U2AF 65 kda subunit	protein	174	24% helix, 31% strand	P26368
P, E	DNA (5'-D(UPUPUPUP(BRU)PCP*U)-3')	dna	7	—	—

Ligands and binding sites

CPQ · N,N-bis(3-D-gluconamidopropyl)deoxycholamide · ligand · chains B
SO4 · Sulfate ion · ion · 6 copies · chains A, P, B
DIO · 1,4-diethylene dioxide · additive · 5 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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	85	0.42	0.79	22	empty
2	86	0.40	0.78	28	empty
3	108	0.36	0.74	16	SO4

Interfaces

4 interfaces between chains.

B–E · 543 Å² buried · 17 hydrogen bonds · protein-nucleic
A–P · 540 Å² buried · 17 hydrogen bonds · protein-nucleic
B–P · 483 Å² buried · 9 hydrogen bonds · protein-nucleic
A–B · 326 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

3VAJ · Structure of U2AF65 variant with BrU5C6 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 3VAJ · PDBe 3VAJ · UniProt P26368

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