MolNFT v1 · #115882 · protein
Crystal structure of the intact chaetomium thermophilum NSP1-NUP49- NUP57 channel nucleoporin heterotrimer bound to its NIC96 nuclear pore complex attachment site
5CWS · Sab-158 Fab light chain: “Crystal structure of the intact chaetomium thermophilum NSP1-NUP49- NUP57 channel nucleoporin heterotrimer…”. X-ray diffraction, 1 ligand (OS), 20 pockets (best druggability 0.79). MolNFT v1 #115882 on…
- PDB
- 5CWS
- Type
- protein
- Length
- 2,122 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sab-158 Fab light chain; Sab-158 Fab heavy chain; Nucleoporin NSP1; Nucleoporin NUP49…
- UniProt
- G0SBQ3, G0S4X2, G0S0R2, G0S024
- Ligands
- OS
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Sab-158 Fab light chain | protein | 208 | 2% helix, 49% strand | — |
| B, H | Sab-158 Fab heavy chain | protein | 223 | 3% helix, 49% strand | — |
| C, I | Nucleoporin NSP1 | protein | 169 | 93% helix, 0% strand | G0SBQ3 |
| D, J | Nucleoporin NUP49 | protein | 180 | 94% helix, 0% strand | G0S4X2 |
| E, K | Nucleoporin NUP57 | protein | 241 | 71% helix, 6% strand | G0S0R2 |
| F, L | Nucleoporin NIC96 | protein | 40 | 53% helix, 0% strand | G0S024 |
Ligands and binding sites
- OS · Osmium ion · metal · 2 copies · chains C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.79 | 0.80 | 104 | empty |
| 2 | 670 | 0.78 | 0.83 | 65 | empty |
| 3 | 1021 | 0.75 | 0.77 | 80 | empty |
| 4 | 767 | 0.75 | 0.79 | 71 | empty |
| 5 | 525 | 0.74 | 0.82 | 71 | empty |
Interfaces
34 interfaces between chains.
- C–E · 4309 Ų buried · 25 hydrogen bonds · protein-protein
- I–K · 4220 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 3797 Ų buried · 28 hydrogen bonds · protein-protein
- J–K · 3687 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2890 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5CWS · Crystal structure of the intact Chaetomium thermophilum Nsp1-Nup49-Nup57 channel… · the same entry in another collection · chain L against L, 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 G0SBQ3
- Every structure of UniProt G0S4X2
- Every structure of UniProt G0S0R2
- Every structure of UniProt G0S024
- Elsewhere: RCSB PDB 5CWS · PDBe 5CWS · UniProt G0SBQ3 · UniProt G0S4X2 · UniProt G0S0R2 · UniProt G0S024
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