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Structural insights into yeast NIT2: C169S mutant of yeast NIT2 in complex with an endogenous peptide-like ligand
Analyse Structural insights into yeast NIT2: C169S mutant of 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
- 4HGD
- Type
- protein
- Length
- 1,193 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
- KGT
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 299 | 35% helix, 26% strand | P47016 |
| B | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 300 | 35% helix, 28% strand | P47016 |
| C | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 302 | 37% helix, 27% strand | P47016 |
| D | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 292 | 34% helix, 27% strand | P47016 |
Ligands and binding sites
- KGT · N-(4-carboxy-4-oxobutanoyl)-L-cysteinylglycine · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 13 copies · chains A, B, D, C
- CAC · Cacodylate ion · additive · 4 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 | 201 | 0.71 | 0.88 | 31 | KGT |
| 2 | 234 | 0.70 | 0.86 | 32 | KGT |
| 3 | 252 | 0.70 | 0.85 | 38 | KGT |
| 4 | 325 | 0.70 | 0.83 | 38 | KGT |
| 5 | 764 | 0.70 | 0.76 | 51 | GOL, CAC |
Interfaces
4 interfaces between chains.
- B–C · 1943 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1934 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 774 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 85 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4HGD · Structural insights into yeast Nit2: C169S mutant of yeast Nit2 in complex with an… · the same entry in another collection · chain D against D, TM-score 1.00
- P47016 · AlphaFold monomer V2.0 prediction for deaminated glutathione amidase (P47016) · a predicted model of the same protein · chain C 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 4HGD · PDBe 4HGD · UniProt P47016
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