Research workbench
Structural insights into yeast Nit2: wild-type yeast Nit2
Analyse Structural insights into yeast Nit2: wild-type yeast Nit2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H5U
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.92
- Source
- Saccharomyces cerevisiae
- Molecule
- Probable hydrolase NIT2
- EC
- 3.5.-.-
- UniProt
- P47016
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.92 · 3 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 303 | 36% helix, 26% strand | P47016 |
| C | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 296 | 38% helix, 26% strand | P47016 |
| D | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 302 | 35% helix, 26% strand | P47016 |
Ligands and binding sites
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D
- CAC · Cacodylate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.76 | 0.84 | 44 | GOL |
| 2 | 923 | 0.73 | 0.77 | 83 | GOL |
| 3 | 638 | 0.72 | 0.79 | 62 | empty |
| 4 | 278 | 0.66 | 0.82 | 41 | empty |
| 5 | 201 | 0.58 | 0.81 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 831 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 210 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 108 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 102 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
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 P47016
- Elsewhere: RCSB PDB 4H5U · PDBe 4H5U · UniProt P47016
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