Research workbench
Architecture of a coat for the nuclear pore membrane
Analyse Architecture of a coat for the nuclear pore membrane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BG1
- Type
- protein
- Length
- 2,822 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SEC13 homolog; Nucleoporin NUP145
- EC
- 3.4.21.-
- UniProt
- P55735, P49687
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Protein SEC13 homolog | protein | 285 | 2% helix, 46% strand | P55735 |
| B, F | Nucleoporin NUP145 (EC 3.4.21.-) | protein | 423 | 58% helix, 4% strand | P49687 |
| C, G | Nucleoporin NUP145 (EC 3.4.21.-) | protein | 420 | 58% helix, 6% strand | P49687 |
| D, H | Protein SEC13 homolog | protein | 283 | 2% helix, 45% strand | P55735 |
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 | 783 | 0.86 | 0.89 | 62 | empty |
| 2 | 1027 | 0.86 | 0.87 | 88 | empty |
| 3 | 1176 | 0.84 | 0.85 | 85 | empty |
| 4 | 1191 | 0.84 | 0.85 | 92 | empty |
| 5 | 1116 | 0.83 | 0.84 | 103 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2836 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2824 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2687 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2684 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1662 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3BG1 · Architecture of a Coat for the Nuclear Pore Membrane · the same entry in another collection · chain H against H, TM-score 1.00
- P55735 · AlphaFold monomer V2.0 prediction for protein SEC13 homolog (P55735) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P49687 · AlphaFold monomer V2.0 prediction for nucleoporin NUP145 (P49687) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P55735
- Every structure of UniProt P49687
- Elsewhere: RCSB PDB 3BG1 · PDBe 3BG1 · UniProt P55735 · UniProt P49687
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