MolNFT v1 · #69064 · protein
Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from saccharomyces cerevisiae in the hexagonal, P61 space group
3KES · Nucleoporin NUP145: “Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from…”. X-ray diffraction, 4 pockets (best druggability 0.59). MolNFT v1 #69064 on GenesisL1: 3D structure, binding…
- PDB
- 3KES
- Type
- protein
- Length
- 295 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 · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoporin NUP145 (EC 3.4.21.-) | protein | 142 | 23% helix, 29% strand | P49687 |
| B | Nucleoporin NUP145 (EC 3.4.21.-) | protein | 153 | 25% helix, 28% strand | P49687 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 22 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.59 | 0.84 | 33 | EDO |
| 2 | 110 | 0.40 | 0.75 | 21 | empty |
| 3 | 79 | 0.34 | 0.74 | 18 | empty |
| 4 | 69 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1055 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3KES · 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 0.93
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 3KES · PDBe 3KES · UniProt P49687
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