Research workbench
Cleavage and polyadenylation specificity factor subunit 3 (CPSF3) in complex with nvp-LTM531
Analyse Cleavage and polyadenylation specificity factor subunit 3 (CPSF3) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M8Q
- Type
- protein
- Length
- 904 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cleavage and polyadenylation specificity factor subunit 3
- EC
- 3.1.27.-
- UniProt
- Q9UKF6
- Ligands
- JBG, ZN, PO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cleavage and polyadenylation specificity factor subunit 3 (EC 3.1.27.-) | protein | 451 | 33% helix, 23% strand | Q9UKF6 |
| B | Cleavage and polyadenylation specificity factor subunit 3 (EC 3.1.27.-) | protein | 453 | 31% helix, 22% strand | Q9UKF6 |
Ligands and binding sites
- JBG · N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.85 | 0.91 | 52 | JBG, PO4 |
| 2 | 443 | 0.84 | 0.91 | 52 | JBG, PO4 |
| 3 | 289 | 0.65 | 0.82 | 40 | empty |
| 4 | 325 | 0.63 | 0.79 | 58 | PO4 |
| 5 | 115 | 0.43 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 965 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6M8Q · Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKF6 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9UKF6
- Elsewhere: RCSB PDB 6M8Q · PDBe 6M8Q · UniProt Q9UKF6
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