Research workbench
Crystal structure of the heterotrimeric SEC13-NUP145C-NUP84 nucleoporin complex
Analyse Crystal structure of the heterotrimeric SEC13-NUP145C-NUP84 nucleoporin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IKO
- Type
- protein
- Length
- 3,351 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC13; Nucleoporin NUP145C; Nucleoporin NUP84
- EC
- 3.4.21.-
- UniProt
- Q04491, P49687, P52891
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Protein transport protein SEC13 | protein | 274 | 1% helix, 42% strand | Q04491 |
| B | Nucleoporin NUP145C (EC 3.4.21.-) | protein | 434 | 57% helix, 4% strand | P49687 |
| C | Nucleoporin NUP84 | protein | 419 | 65% helix, 1% strand | P52891 |
| E | Nucleoporin NUP145C (EC 3.4.21.-) | protein | 423 | 56% helix, 4% strand | P49687 |
| F | Nucleoporin NUP84 | protein | 419 | 65% helix, 1% strand | P52891 |
| H | Nucleoporin NUP145C (EC 3.4.21.-) | protein | 420 | 56% helix, 4% strand | P49687 |
| I | Nucleoporin NUP84 | protein | 414 | 65% helix, 1% strand | P52891 |
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 | 1003 | 0.85 | 0.86 | 75 | empty |
| 2 | 1093 | 0.83 | 0.84 | 87 | empty |
| 3 | 935 | 0.83 | 0.84 | 68 | empty |
| 4 | 530 | 0.76 | 0.84 | 60 | empty |
| 5 | 924 | 0.75 | 0.78 | 92 | empty |
Interfaces
12 interfaces between chains.
- D–E · 2738 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2707 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2567 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 2087 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2065 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3IKO · Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex · the same entry in another collection · chain I against I, TM-score 1.00
- P52891 · AlphaFold monomer V2.0 prediction for nucleoporin NUP84 (P52891) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P49687 · AlphaFold monomer V2.0 prediction for nucleoporin NUP145 (P49687) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q04491
- Every structure of UniProt P49687
- Every structure of UniProt P52891
- Elsewhere: RCSB PDB 3IKO · PDBe 3IKO · UniProt Q04491 · UniProt P49687 · UniProt P52891
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