MolNFT v1 · #115495 · protein
Truncated ran wild type in complex with GDP-bef and RANBD1
5CLL · GTP-binding nuclear protein ran: “Truncated ran wild type in complex with GDP-bef and RANBD1”. X-ray diffraction, 3 ligands (GDP, BEF, MG), 6 pockets (best druggability 0.55). MolNFT v1 #115495 on GenesisL1: 3D structure, binding…
- PDB
- 5CLL
- Type
- protein
- Length
- 636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; E3 sumo-protein ligase RANBP2
- EC
- 6.3.2.-
- UniProt
- P62826, P49792
- Ligands
- GDP, BEF, MG
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | GTP-binding nuclear protein ran | protein | 179 | 29% helix, 26% strand | P62826 |
| B, D | E3 sumo-protein ligase RANBP2 (EC 6.3.2.-) | protein | 139 | 11% helix, 47% strand | P49792 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- BEF · Beryllium trifluoride ion · 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.55 | 0.83 | 30 | GDP, BEF, MG |
| 2 | 120 | 0.53 | 0.82 | 28 | GDP, BEF, MG |
| 3 | 100 | 0.42 | 0.77 | 17 | empty |
| 4 | 106 | 0.41 | 0.76 | 13 | empty |
| 5 | 76 | 0.36 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1935 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1916 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
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 5CLL · PDBe 5CLL · UniProt P62826 · UniProt P49792
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