Research workbench
Structural insights into yeast NIT2: wild-type yeast NIT2 in complex with oxaloacetate
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
- 4HG5
- Type
- protein
- Length
- 1,200 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
- OAA
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 304 | 34% helix, 27% strand | P47016 |
| B | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 302 | 35% helix, 26% strand | P47016 |
| C | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 301 | 35% helix, 28% strand | P47016 |
| D | Probable hydrolase NIT2 (EC 3.5.-.-) | protein | 293 | 32% helix, 27% strand | P47016 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.73 | 0.78 | 57 | CAC |
| 2 | 316 | 0.71 | 0.84 | 42 | OAA |
| 3 | 318 | 0.70 | 0.83 | 40 | OAA |
| 4 | 278 | 0.70 | 0.84 | 37 | OAA |
| 5 | 323 | 0.69 | 0.83 | 44 | OAA |
Interfaces
4 interfaces between chains.
- B–D · 1941 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1927 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 892 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 86 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4HG5 · Structural insights into yeast Nit2: wild-type yeast Nit2 in complex with oxaloacetate · 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 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 4HG5 · PDBe 4HG5 · UniProt P47016
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