Research workbench
Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from saccharomyces cerevisiae
Analyse Crystal structure of the autoproteolytic domain from the nuclear pore complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KEP
- Type
- protein
- Length
- 292 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin NUP145
- EC
- 3.4.21.-
- UniProt
- P49687
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoporin NUP145 (EC 3.4.21.-) | protein | 144 | 20% helix, 28% strand | P49687 |
| B | Nucleoporin NUP145 (EC 3.4.21.-) | protein | 148 | 20% helix, 29% strand | P49687 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.59 | 0.84 | 29 | empty |
| 2 | 146 | 0.58 | 0.83 | 29 | empty |
| 3 | 102 | 0.37 | 0.74 | 27 | EDO |
| 4 | 66 | 0.34 | 0.76 | 18 | EDO |
Interfaces
1 interface between chains.
- A–B · 1053 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3KEP · Crystal structure of the autoproteolytic domain from the nuclear pore complex component… · the same entry in another collection · chain A against A, TM-score 1.00
- P49687 · AlphaFold monomer V2.0 prediction for nucleoporin NUP145 (P49687) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P49687
- Elsewhere: RCSB PDB 3KEP · PDBe 3KEP · UniProt P49687
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