MolNFT v1 · #82046 · protein + DNA
Structure of U2AF65 variant with BRU5C1 DNA
3VAL · Splicing factor U2AF 65 kda subunit: “Structure of U2AF65 variant with BRU5C1 DNA”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.58). MolNFT v1 #82046 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3VAL
- Type
- protein + DNA
- Length
- 716 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Splicing factor U2AF 65 kda subunit; DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*U)-3')
- UniProt
- P26368
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Splicing factor U2AF 65 kda subunit | protein | 174 | 24% helix, 31% strand | P26368 |
| B | Splicing factor U2AF 65 kda subunit | protein | 173 | 25% helix, 31% strand | P26368 |
| I | Splicing factor U2AF 65 kda subunit | protein | 172 | 27% helix, 30% strand | P26368 |
| E, H, K | DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*U)-3') | dna | 6 | — | — |
| P | DNA (5'-D(*C*UP*UP*UP*(BRU)P*UP*U)-3') | dna | 5 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, D, I, K
- DIO · 1,4-diethylene dioxide · additive · 4 copies · chains A, B, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.58 | 0.76 | 39 | empty |
| 2 | 160 | 0.48 | 0.77 | 25 | empty |
| 3 | 55 | 0.46 | 0.84 | 22 | empty |
| 4 | 127 | 0.38 | 0.73 | 16 | SO4 |
| 5 | 72 | 0.29 | 0.73 | 15 | SO4 |
Interfaces
10 interfaces between chains.
- A–P · 606 Ų buried · 21 hydrogen bonds · protein-nucleic
- I–K · 591 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–K · 464 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–H · 439 Ų buried · 5 hydrogen bonds · protein-nucleic
- I–E · 432 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 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 3VAL · PDBe 3VAL · UniProt P26368
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.