Research workbench
Structure of U2AF65 variant with BRU5C2 DNA
Analyse Structure of U2AF65 variant with BRU5C2 DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VAM
- 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*CP*UP*UP*(BRU)P*UP*U)-3')
- UniProt
- P26368
- Ligands
- CPQ, SO4
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Splicing factor U2AF 65 kda subunit | protein | 174 | 24% helix, 31% strand | P26368 |
| B | Splicing factor U2AF 65 kda subunit | protein | 172 | 27% helix, 31% strand | P26368 |
| P, E | DNA (5'-D(*UP*CP*UP*UP*(BRU)P*UP*U)-3') | dna | 6 | — | — |
Ligands and binding sites
- CPQ · N,N-bis(3-D-gluconamidopropyl)deoxycholamide · ligand · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, P, B, E
- 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.49 | 0.77 | 29 | empty |
| 2 | 75 | 0.41 | 0.80 | 18 | empty |
| 3 | 74 | 0.31 | 0.74 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–E · 592 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 589 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–P · 481 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 287 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 3VAM · PDBe 3VAM · UniProt P26368
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