Research workbench
Crystal structure of the ZNF8 of nucleoporin NUP358/RANBP2 in complex with ran-GDP
Analyse Crystal structure of the ZNF8 of nucleoporin NUP358/RANBP2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MNV
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; E3 sumo-protein ligase RANBP2
- UniProt
- P62826, P49792
- Ligands
- GDP, MG, ZN
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 203 | 36% helix, 26% strand | P62826 |
| B | E3 sumo-protein ligase RANBP2 | protein | 38 | 0% helix, 16% strand | P49792 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ZN · Zinc ion · metal · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.38 | 0.75 | 22 | empty |
| 2 | 65 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 854 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7MNV · Crystal Structure of the ZnF8 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP · 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 7MNV · PDBe 7MNV · UniProt P62826 · UniProt P49792
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