Research workbench
Crystal structure of the ZNF3 of nucleoporin NUP153 in complex with ran-GDP, resolution 2.05 ångström
Analyse Crystal structure of the ZNF3 of nucleoporin NUP153 in complex with ran-GDP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MO3
- Type
- protein
- Length
- 487 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; Nuclear pore complex protein NUP153
- UniProt
- P62826, P49791
- Ligands
- GDP, MG, ZN
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 204 | 35% helix, 27% strand | P62826 |
| B, D | Nuclear pore complex protein NUP153 | protein | 38 | 11% helix, 16% strand | P49791 |
| C | GTP-binding nuclear protein ran | protein | 207 | 35% 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.56 | 0.81 | 42 | empty |
| 2 | 117 | 0.53 | 0.82 | 20 | empty |
| 3 | 135 | 0.51 | 0.80 | 17 | empty |
| 4 | 73 | 0.36 | 0.77 | 18 | empty |
| 5 | 64 | 0.34 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–D · 828 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 786 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 583 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7MO3 · Crystal Structure of the ZnF3 of Nucleoporin NUP153 in complex with Ran-GDP, resolution… · the same entry in another collection · chain A against A, TM-score 1.00
- P49791 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP153 (P49791) · a predicted model of the same protein · chain B against A, TM-score 0.74
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 P49791
- Elsewhere: RCSB PDB 7MO3 · PDBe 7MO3 · UniProt P62826 · UniProt P49791
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