MolNFT v1 · #69581 · protein
Crystal structure of the mlle domain of POLY(A)-binding protein
3KUR · Polyadenylate-binding protein 1: “Crystal structure of the mlle domain of POLY(A)-binding protein”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.68). MolNFT v1 #69581 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KUR
- Type
- protein
- Length
- 578 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyadenylate-binding protein 1
- UniProt
- P11940
- Ligands
- CL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, H | Polyadenylate-binding protein 1 | protein | 73 | 77% helix, 0% strand | P11940 |
| C, E, F, G | Polyadenylate-binding protein 1 | protein | 72 | 79% helix, 0% strand | P11940 |
| D | Polyadenylate-binding protein 1 | protein | 71 | 82% helix, 0% strand | P11940 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.68 | 0.82 | 44 | empty |
| 2 | 311 | 0.66 | 0.81 | 43 | CL |
| 3 | 380 | 0.66 | 0.80 | 60 | empty |
Interfaces
14 interfaces between chains.
- G–H · 688 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 686 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 659 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 658 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 420 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3KUR · Crystal structure of the MLLE domain of poly(A)-binding protein · the same entry in another collection · chain H against H, TM-score 1.00
- P11940 · AlphaFold monomer V2.0 prediction for polyadenylate-binding protein 1 (P11940) · a predicted model of the same protein · chain D 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 P11940
- Elsewhere: RCSB PDB 3KUR · PDBe 3KUR · UniProt P11940
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