MolNFT v1 · #55063 · protein
Structure of the ran-binding domain from human RANBP3 (E352A-R353V double mutant)
2Y8G · Ran-binding protein 3: “Structure of the ran-binding domain from human RANBP3 (E352A-R353V double mutant)”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.68). MolNFT v1 #55063 on GenesisL1: 3D structure, binding…
- PDB
- 2Y8G
- Type
- protein
- Length
- 240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ran-binding protein 3
- UniProt
- Q9H6Z4
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ran-binding protein 3 | protein | 122 | 21% helix, 49% strand | Q9H6Z4 |
| B | Ran-binding protein 3 | protein | 118 | 19% helix, 56% strand | Q9H6Z4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.68 | 0.93 | 25 | empty |
| 2 | 90 | 0.33 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 735 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2Y8G · Structure of the Ran-binding domain from human RanBP3 (E352A-R353V double mutant) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H6Z4 · AlphaFold monomer V2.0 prediction for ran-binding protein 3 (Q9H6Z4) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9H6Z4
- Elsewhere: RCSB PDB 2Y8G · PDBe 2Y8G · UniProt Q9H6Z4
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