MolNFT v1 · #64974 · protein
Crystal structure of human rangdp-NUP153ZNF12 complex
3GJ7 · GTP-binding nuclear protein ran: “Crystal structure of human rangdp-NUP153ZNF12 complex”. X-ray diffraction, 3 ligands (GDP, MG, ZN), 3 pockets (best druggability 0.41). MolNFT v1 #64974 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3GJ7
- Type
- protein
- Length
- 457 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 NUP153
- UniProt
- P62826, P49791
- Ligands
- GDP, MG, ZN
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 201 | 35% helix, 27% strand | P62826 |
| B, D | Nuclear pore complex protein NUP153 | protein | 27 | 0% helix, 22% strand | P49791 |
| C | GTP-binding nuclear protein ran | protein | 202 | 34% helix, 27% strand | P62826 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 6 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.41 | 0.78 | 18 | empty |
| 2 | 77 | 0.36 | 0.76 | 19 | empty |
| 3 | 73 | 0.35 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 515 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 506 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 474 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3GJ7 · Crystal structure of human RanGDP-Nup153ZnF12 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P49791 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP153 (P49791) · a predicted model of the same protein · chain B against A, TM-score 0.79
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 P49791
- Elsewhere: RCSB PDB 3GJ7 · PDBe 3GJ7 · UniProt P62826 · UniProt P49791
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