Research workbench
Crystal structure of SESTRIN2 in complex with nv-0005138
Analyse Crystal structure of SESTRIN2 in complex with nv-0005138 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N0M
- Type
- protein
- Length
- 1,824 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Homo sapiens
- Molecule
- Sestrin-2
- EC
- 1.11.1.15
- UniProt
- P58004
- Ligands
- K94
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · resolution 3.3 · 5 distinct chains · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sestrin-2 (EC 1.11.1.15) | protein | 366 | 66% helix, 2% strand | P58004 |
| B | Sestrin-2 (EC 1.11.1.15) | protein | 365 | 65% helix, 2% strand | P58004 |
| C | Sestrin-2 (EC 1.11.1.15) | protein | 364 | 66% helix, 2% strand | P58004 |
| D | Sestrin-2 (EC 1.11.1.15) | protein | 364 | 65% helix, 3% strand | P58004 |
| E | Sestrin-2 (EC 1.11.1.15) | protein | 365 | 66% helix, 2% strand | P58004 |
Ligands and binding sites
- K94 · 4-(difluoromethyl)-L-leucine · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.72 | 0.97 | 17 | K94 |
| 2 | 58 | 0.71 | 0.98 | 17 | K94 |
| 3 | 64 | 0.71 | 0.97 | 19 | K94 |
| 4 | 59 | 0.70 | 0.96 | 19 | K94 |
| 5 | 59 | 0.70 | 0.97 | 19 | K94 |
Interfaces
5 interfaces between chains.
- B–D · 349 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 345 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 341 Ų buried · 1 hydrogen bond · protein-protein
- B–E · 315 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 298 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P58004
- Elsewhere: RCSB PDB 6N0M · PDBe 6N0M · UniProt P58004
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