MolNFT v1 · #182344 · protein
Crystal structure of nucleoporin NUP50 ran-binding domain in complex with ran-gppnhp
7MO0 · GTP-binding nuclear protein ran: “Crystal structure of nucleoporin NUP50 ran-binding domain in complex with ran-gppnhp”. X-ray diffraction, 3 ligands (GNP, MG, SO4), 8 pockets (best druggability 0.75). MolNFT v1 #182344 on…
- PDB
- 7MO0
- Type
- protein
- Length
- 671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; Nuclear pore complex protein NUP50
- UniProt
- P62826, Q9UKX7
- Ligands
- GNP, MG, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 211 | 27% helix, 24% strand | P62826 |
| B | Nuclear pore complex protein NUP50 | protein | 126 | 13% helix, 43% strand | Q9UKX7 |
| C | GTP-binding nuclear protein ran | protein | 210 | 27% helix, 23% strand | P62826 |
| D | Nuclear pore complex protein NUP50 | protein | 124 | 13% helix, 44% strand | Q9UKX7 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.75 | 0.78 | 110 | GNP, MG |
| 2 | 862 | 0.75 | 0.78 | 92 | GNP, MG |
| 3 | 50 | 0.53 | 0.89 | 19 | empty |
| 4 | 75 | 0.43 | 0.80 | 16 | empty |
| 5 | 73 | 0.36 | 0.77 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2169 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2089 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 538 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 7MO0 · Crystal Structure of Nucleoporin NUP50 Ran-Binding Domain in Complex with Ran-GPPNHP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKX7 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP50 (Q9UKX7) · a predicted model of the same protein · chain D 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 P62826
- Every structure of UniProt Q9UKX7
- Elsewhere: RCSB PDB 7MO0 · PDBe 7MO0 · UniProt P62826 · UniProt Q9UKX7
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