Research workbench
Crystal structure of the complex between the 25 kda subunit and the 59 kda subunit (rrm domain) of human cleavage factor im
Analyse Crystal structure of the complex between the 25 kda subunit and the 59 kda… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N9U
- Type
- protein
- Length
- 590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cleavage and polyadenylation specificity factor subunit 5; Cleavage and polyadenylation…
- UniProt
- O43809, Q8N684
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cleavage and polyadenylation specificity factor subunit 5 | protein | 206 | 23% helix, 37% strand | O43809 |
| B | Cleavage and polyadenylation specificity factor subunit 5 | protein | 201 | 23% helix, 38% strand | O43809 |
| C | Cleavage and polyadenylation specificity factor subunit 7 | protein | 96 | 36% helix, 31% strand | Q8N684 |
| I | Cleavage and polyadenylation specificity factor subunit 7 | protein | 87 | 30% helix, 28% strand | Q8N684 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.69 | 0.78 | 48 | GOL |
| 2 | 550 | 0.68 | 0.78 | 47 | GOL |
| 3 | 181 | 0.53 | 0.78 | 33 | empty |
| 4 | 152 | 0.50 | 0.78 | 31 | empty |
| 5 | 133 | 0.50 | 0.80 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1436 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 584 Ų buried · 14 hydrogen bonds · protein-protein
- A–I · 537 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 331 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 275 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3N9U · Crystal Structure of the Complex between the 25 kDa Subunit and the 59 kDa Subunit (RRM… · the same entry in another collection · chain I against I, TM-score 1.00
- Q8N684 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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 0.99
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
- Every structure of UniProt Q8N684
- Elsewhere: RCSB PDB 3N9U · PDBe 3N9U · UniProt O43809 · UniProt Q8N684
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