MolNFT v1 · #95616 · protein
Crystal structure of a polyadenylate-binding protein 3 (PABPC3) from homo sapiens at 2.30 a resolution
4IVE: “Crystal structure of a polyadenylate-binding protein 3 (PABPC3) from homo sapiens at 2.30 a resolution”. X-ray diffraction, 1 ligand (CL), 1 pocket (best druggability 0.71). MolNFT v1 #95616 on GenesisL1: 3D structure, binding sites…
- PDB
- 4IVE
- Type
- protein
- Length
- 305 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyadenylate-binding protein 3
- UniProt
- Q9H361
- Ligands
- CL
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyadenylate-binding protein 3 | protein | 76 | 72% helix, 0% strand | Q9H361 |
| B | Polyadenylate-binding protein 3 | protein | 77 | 74% helix, 0% strand | Q9H361 |
| C, D | Polyadenylate-binding protein 3 | protein | 76 | 71% helix, 0% strand | Q9H361 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.71 | 0.84 | 49 | empty |
Interfaces
5 interfaces between chains.
- A–B · 850 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 849 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 475 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 380 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 311 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4IVE · Crystal structure of a polyadenylate-binding protein 3 (PABPC3) from Homo sapiens at 2.30… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H361 · AlphaFold monomer V2.0 prediction for polyadenylate-binding protein 3 (Q9H361) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q9H361
- Elsewhere: RCSB PDB 4IVE · PDBe 4IVE · UniProt Q9H361
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