Research workbench
Crystal structure of yeast GNA1 bound to CoA and glnac-6P
Analyse Crystal structure of yeast GNA1 bound to CoA and glnac-6P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I1D
- Type
- protein
- Length
- 626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosamine-phosphate N-acetyltransferase
- EC
- 2.3.1.4
- UniProt
- P43577
- Ligands
- 16G, COA
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosamine-phosphate N-acetyltransferase (EC 2.3.1.4) | protein | 156 | 36% helix, 34% strand | P43577 |
| B | Glucosamine-phosphate N-acetyltransferase (EC 2.3.1.4) | protein | 154 | 36% helix, 37% strand | P43577 |
| C | Glucosamine-phosphate N-acetyltransferase (EC 2.3.1.4) | protein | 155 | 35% helix, 36% strand | P43577 |
| D | Glucosamine-phosphate N-acetyltransferase (EC 2.3.1.4) | protein | 161 | 36% helix, 35% strand | P43577 |
Ligands and binding sites
- 16G · 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · 3 copies · chains A, D, B, C
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.78 | 0.80 | 79 | 16G, COA |
| 2 | 328 | 0.63 | 0.79 | 44 | empty |
| 3 | 293 | 0.60 | 0.78 | 36 | 16G |
| 4 | 66 | 0.29 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–D · 3037 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 2995 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 313 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1I1D · Crystal structure of yeast GNA1 bound to CoA and glnac-6P · the same entry in another collection · chain D against D, TM-score 1.00
- P43577 · AlphaFold monomer V2.0 prediction for glucosamine 6-phosphate N-acetyltransferase (P43577) · a predicted model of the same protein · chain A 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 P43577
- Elsewhere: RCSB PDB 1I1D · PDBe 1I1D · UniProt P43577
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.