MolNFT v1 · #132682 · protein
Pandda analysis group deposition -- crystal structure of human cleavage factor im in complex with FMOPL000589A
5R67 · Cleavage and polyadenylation specificity factor subunit 5: “Pandda analysis group deposition -- crystal structure of human cleavage factor im in complex with FMOPL000589A”. X-ray diffraction, 2 ligands (S6V, ZN), 4 pockets (best…
- PDB
- 5R67
- Type
- protein
- Length
- 394 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
- S6V, ZN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cleavage and polyadenylation specificity factor subunit 5 | protein | 197 | 24% helix, 38% strand | O43809 |
Ligands and binding sites
- S6V · 1-[2-(2-oxidanylidenepyrrolidin-1-yl)ethyl]-3-phenyl-urea · ligand · chains A
- ZN · Zinc ion · metal · 6 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.72 | 0.80 | 39 | S6V |
| 2 | 504 | 0.67 | 0.78 | 40 | empty |
| 3 | 610 | 0.65 | 0.76 | 47 | ZN |
| 4 | 74 | 0.38 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 203 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5R67 · 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 0.99
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
- Elsewhere: RCSB PDB 5R67 · PDBe 5R67 · UniProt O43809
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