MolNFT v1 · #115500 · protein
Ran Y39A in complex with gppnhp and RANBD1
5CLQ · GTP-binding nuclear protein ran: “Ran Y39A in complex with gppnhp and RANBD1”. X-ray diffraction, 3 ligands (GNP, MG, SO4), 13 pockets (best druggability 0.69). MolNFT v1 #115500 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5CLQ
- Type
- protein
- Length
- 672 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
- GNP, MG, SO4
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 207 | 28% helix, 23% strand | P62826 |
| B | E3 sumo-protein ligase RANBP2 (EC 6.3.2.-) | protein | 134 | 12% helix, 46% strand | P49792 |
| C | GTP-binding nuclear protein ran | protein | 200 | 26% helix, 24% strand | P62826 |
| D | E3 sumo-protein ligase RANBP2 (EC 6.3.2.-) | protein | 131 | 11% helix, 44% strand | P49792 |
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 · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.69 | 0.78 | 60 | empty |
| 2 | 263 | 0.66 | 0.82 | 32 | empty |
| 3 | 548 | 0.65 | 0.76 | 55 | empty |
| 4 | 229 | 0.58 | 0.79 | 31 | empty |
| 5 | 149 | 0.51 | 0.80 | 29 | GNP, MG |
Interfaces
6 interfaces between chains.
- C–D · 2214 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2189 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 752 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 200 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CLQ · Ran Y39A in complex with GPPNHP and RanBD1 · 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 5CLQ · PDBe 5CLQ · UniProt P62826 · UniProt P49792
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