Research workbench
Pandda analysis group deposition -- crystal structure of human cleavage factor im in complex with NM466-1
Analyse Pandda analysis group deposition -- crystal structure of human cleavage factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5R4Q
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cleavage and polyadenylation specificity factor subunit 5
- UniProt
- O43809
- Ligands
- RW7, ZN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cleavage and polyadenylation specificity factor subunit 5 | protein | 197 | 24% helix, 38% strand | O43809 |
| B | Cleavage and polyadenylation specificity factor subunit 5 | protein | 196 | 23% helix, 37% strand | O43809 |
Ligands and binding sites
- RW7 · (3S)-3,4-dimethyl-3-propyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione · ligand · chains B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.75 | 0.77 | 84 | ZN |
| 2 | 488 | 0.66 | 0.78 | 42 | RW7 |
| 3 | 61 | 0.37 | 0.78 | 18 | empty |
| 4 | 55 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 198 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5R4Q · PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in… · the same entry in another collection · chain A against A, TM-score 1.00
- O43809 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O43809
- Elsewhere: RCSB PDB 5R4Q · PDBe 5R4Q · UniProt O43809
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