MolNFT v1 · #20842 · protein
Structure of the ran-gppnhp-RANBD1 complex
1RRP: “Structure of the ran-gppnhp-RANBD1 complex”. X-ray diffraction, 2 ligands (GNP, MG), 7 pockets (best druggability 0.61). MolNFT v1 #20842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RRP
- Type
- protein
- Length
- 652 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ran; Nuclear pore complex protein NUP358
- UniProt
- P62826, P49792
- Ligands
- GNP, MG
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ran | protein | 204 | 30% helix, 21% strand | P62826 |
| B, D | Nuclear pore complex protein NUP358 | protein | 134 | 10% helix, 40% strand | P49792 |
| C | Ran | protein | 180 | 27% helix, 24% strand | P62826 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.61 | 0.83 | 34 | empty |
| 2 | 165 | 0.58 | 0.82 | 31 | MG, GNP |
| 3 | 71 | 0.57 | 0.88 | 19 | empty |
| 4 | 152 | 0.55 | 0.81 | 31 | MG, GNP |
| 5 | 100 | 0.44 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2448 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1752 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1RRP · Structure of the ran-gppnhp-RANBD1 complex · the same entry in another collection · chain A against A, TM-score 1.00
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 P49792
- Elsewhere: RCSB PDB 1RRP · PDBe 1RRP · UniProt P62826 · UniProt P49792
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