Research workbench
Crystal structure of the ZNF5 or ZNF6 of nucleoporin NUP358/RANBP2 in complex with ran-GDP
Analyse Crystal structure of the ZNF5 or ZNF6 of nucleoporin NUP358/RANBP2 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MNT
- Type
- protein
- Length
- 479 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
- UniProt
- P62826, P49792
- Ligands
- GDP, MG, ZN
- Pockets
- 7 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 201 | 33% helix, 27% strand | P62826 |
| B, D | E3 sumo-protein ligase RANBP2 | protein | 38 | 0% helix, 16% strand | P49792 |
| C | GTP-binding nuclear protein ran | protein | 202 | 33% helix, 27% strand | P62826 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 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
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.46 | 0.80 | 24 | empty |
| 2 | 51 | 0.43 | 0.84 | 17 | empty |
| 3 | 115 | 0.41 | 0.76 | 22 | empty |
| 4 | 102 | 0.36 | 0.74 | 18 | empty |
| 5 | 60 | 0.36 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 829 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 818 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 550 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7MNT · Crystal Structure of the ZnF5 or ZnF6 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 7MNT · PDBe 7MNT · UniProt P62826 · UniProt P49792
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