Research workbench
Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase from mycobacterium smegmatis.
Analyse Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FV3
- Type
- protein
- Length
- 1,484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-6-phosphate deacetylase
- EC
- 3.5.1.25
- UniProt
- A0QU89
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) | protein | 378 | 31% helix, 27% strand | A0QU89 |
| D | N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) | protein | 350 | 33% helix, 24% strand | A0QU89 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.66 | 0.86 | 38 | empty |
| 2 | 182 | 0.59 | 0.82 | 34 | empty |
| 3 | 139 | 0.58 | 0.84 | 33 | empty |
| 4 | 69 | 0.48 | 0.84 | 17 | empty |
| 5 | 58 | 0.45 | 0.84 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1043 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1016 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 276 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 266 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6FV3 · Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase from Mycobacterium… · the same entry in another collection · chain C against C, TM-score 1.00
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 A0QU89
- Elsewhere: RCSB PDB 6FV3 · PDBe 6FV3 · UniProt A0QU89
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.