Research workbench
Structural insights into yeast NIT2: wild-type yeast NIT2 in complex with alpha-ketoglutarate
Analyse Structural insights into yeast NIT2: wild-type yeast NIT2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HG3
- Type
- protein
- Length
- 1,202 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable hydrolase NIT2
- EC
- 3.5.-.-
- UniProt
- P47016
- Ligands
- AKG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 304 | 36% helix, 27% strand | P47016 |
| B, C | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 303 | 36% helix, 26% strand | P47016 |
| D | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 292 | 35% helix, 28% strand | P47016 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D
- CAC · Cacodylate ion · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.78 | 0.80 | 79 | GOL, CAC |
| 2 | 283 | 0.70 | 0.84 | 39 | AKG, GOL, CAC |
| 3 | 297 | 0.69 | 0.84 | 37 | CAC |
| 4 | 281 | 0.68 | 0.83 | 39 | CAC |
| 5 | 314 | 0.67 | 0.82 | 38 | CAC |
Interfaces
4 interfaces between chains.
- B–D · 1995 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1956 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 851 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 109 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4HG3 · Structural insights into yeast Nit2: wild-type yeast Nit2 in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P47016 · AlphaFold monomer V2.0 prediction for deaminated glutathione amidase (P47016) · a predicted model of the same protein · chain D 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 P47016
- Elsewhere: RCSB PDB 4HG3 · PDBe 4HG3 · UniProt P47016
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