Research workbench
Cryo-EM structure of the NR subunit from X. laevis NPC
Analyse Cryo-EM structure of the NR subunit from X. laevis NPC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WB4
- Type
- protein
- Length
- 18,879 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 5.6
- Source
- Xenopus laevis
- Molecule
- outer Nup133; Nuclear pore complex protein Nup85; MGC154553 protein; MGC83926 protein…
- UniProt
- A0A1L8H1I9, Q68FJ0, Q05AW3, Q66IZ6, Q6GNF1, A0A1L8GIX3, Q7ZWL0, Q7ZYJ8, A0A1L8HBE3, A2RV69, Q7ZX96, Q642R6, Q5U249
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 5.6 · 23 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, P | outer Nup133 | protein | 1021 | 41% helix, 18% strand | A0A1L8H1I9 |
| B | Nuclear pore complex protein Nup85 | protein | 628 | 73% helix, 2% strand | Q68FJ0 |
| C | MGC154553 protein | protein | 343 | 2% helix, 48% strand | Q05AW3 |
| F | MGC83926 protein | protein | 318 | 0% helix, 53% strand | Q66IZ6 |
| d | Nucleoporin SEH1-B | protein | 320 | 2% helix, 44% strand | Q6GNF1 |
| b | Nuclear pore complex protein Nup85 | protein | 636 | 71% helix, 2% strand | Q68FJ0 |
| c | MGC154553 protein | protein | 346 | 3% helix, 49% strand | Q05AW3 |
| E | outer Nup160 | protein | 1363 | 47% helix, 15% strand | A0A1L8GIX3 |
| e | outer Nup160 | protein | 1310 | 49% helix, 15% strand | A0A1L8GIX3 |
| f | MGC83926 protein | protein | 321 | 0% helix, 53% strand | Q66IZ6 |
| K | Nup155-prov protein | protein | 330 | 77% helix, 0% strand | Q7ZWL0 |
| H | GATOR complex protein SEC13 | protein | 306 | 2% helix, 51% strand | Q7ZYJ8 |
| G | Nuclear pore complex protein Nup96 | protein | 618 | 58% helix, 2% strand | A0A1L8HBE3 |
| h | GATOR complex protein SEC13 | protein | 307 | 2% helix, 51% strand | Q7ZYJ8 |
| g | Nuclear pore complex protein Nup96 | protein | 672 | 57% helix, 2% strand | A0A1L8HBE3 |
| I, i, M | Nuclear pore complex protein | protein | 796 | 68% helix, 1% strand | A2RV69 |
| L | Nuclear pore complex protein Nup93 | protein | 641 | 67% helix, 3% strand | Q7ZX96 |
| A | MGC83295 protein | protein | 1796 | 69% helix, 1% strand | Q642R6 |
| D | Nucleoporin SEH1-B | protein | 318 | 2% helix, 44% strand | Q6GNF1 |
| O | Nuclear pore complex protein Nup93 | protein | 50 | 96% helix, 0% strand | Q7ZX96 |
| p, j | outer Nup133 | protein | 995 | 41% helix, 18% strand | A0A1L8H1I9 |
| n | Protein ELYS | protein | 910 | 42% helix, 26% strand | Q5U249 |
| N | Protein ELYS | protein | 926 | 41% helix, 25% strand | Q5U249 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.83 | 0.84 | 123 | empty |
| 2 | 980 | 0.82 | 0.83 | 121 | empty |
| 3 | 1182 | 0.82 | 0.83 | 153 | empty |
| 4 | 1502 | 0.81 | 0.83 | 190 | empty |
| 5 | 1977 | 0.81 | 0.83 | 194 | empty |
Interfaces
53 interfaces between chains.
- h–g · 1264 Ų buried · 8 hydrogen bonds · protein-protein
- H–G · 1212 Ų buried · 3 hydrogen bonds · protein-protein
- d–b · 820 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 818 Ų buried · 5 hydrogen bonds · protein-protein
- e–n · 786 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7WB4 · Cryo-EM structure of the nr subunit from X. laevis npc · the same entry in another collection · chain K against K, 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 A0A1L8H1I9
- Every structure of UniProt Q68FJ0
- Every structure of UniProt Q05AW3
- Every structure of UniProt Q66IZ6
- Every structure of UniProt Q6GNF1
- Every structure of UniProt A0A1L8GIX3
- Every structure of UniProt Q7ZWL0
- Every structure of UniProt Q7ZYJ8
- Every structure of UniProt A0A1L8HBE3
- Every structure of UniProt A2RV69
- Every structure of UniProt Q7ZX96
- Every structure of UniProt Q642R6
- Every structure of UniProt Q5U249
- Elsewhere: RCSB PDB 7WB4 · PDBe 7WB4 · UniProt A0A1L8H1I9 · UniProt Q68FJ0 · UniProt Q05AW3 · UniProt Q66IZ6 · UniProt Q6GNF1 · UniProt A0A1L8GIX3 · UniProt Q7ZWL0 · UniProt Q7ZYJ8 · UniProt A0A1L8HBE3 · UniProt A2RV69 · UniProt Q7ZX96 · UniProt Q642R6 · UniProt Q5U249
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