MolNFT v1 · #143598 · protein
Crystal structure of saccharomyces cerevisiae GLE1 ctd-NUP42 gbm complex
6B4E · Nucleoporin GLE1: “Crystal structure of saccharomyces cerevisiae GLE1 ctd-NUP42 gbm complex”. X-ray diffraction, 1 ligand (PRO), 6 pockets (best druggability 0.80). MolNFT v1 #143598 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6B4E
- Type
- protein
- Length
- 662 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin GLE1; Nucleoporin NUP42
- UniProt
- Q12315, P49686
- Ligands
- PRO
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Nucleoporin GLE1 | protein | 296 | 73% helix, 1% strand | Q12315 |
| C | Nucleoporin NUP42 | protein | 39 | 38% helix, 0% strand | P49686 |
| D | Nucleoporin NUP42 | protein | 31 | 35% helix, 0% strand | P49686 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.80 | 0.82 | 89 | empty |
| 2 | 68 | 0.39 | 0.79 | 18 | empty |
| 3 | 97 | 0.38 | 0.76 | 19 | empty |
| 4 | 67 | 0.38 | 0.79 | 18 | EDO |
| 5 | 58 | 0.34 | 0.78 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–C · 852 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 826 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 692 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6B4E · Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q12315 · AlphaFold monomer V2.0 prediction for nucleoporin GLE1 (Q12315) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P49686 · AlphaFold monomer V2.0 prediction for nucleoporin NUP42 (P49686) · a predicted model of the same protein · chain C against A, TM-score 0.78
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 Q12315
- Every structure of UniProt P49686
- Elsewhere: RCSB PDB 6B4E · PDBe 6B4E · UniProt Q12315 · UniProt P49686
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