Research workbench
Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the product complex
Analyse Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DKD
- Type
- protein
- Length
- 1,071 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoacetylglucosamine mutase
- EC
- 5.4.2.3
- UniProt
- Q9P4V2
- Ligands
- NG1, ZN, PO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoacetylglucosamine mutase (EC 5.4.2.3) | protein | 536 | 42% helix, 20% strand | Q9P4V2 |
| B | Phosphoacetylglucosamine mutase (EC 5.4.2.3) | protein | 535 | 42% helix, 20% strand | Q9P4V2 |
Ligands and binding sites
- NG1 · 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-galactopyranose · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.81 | 0.83 | 100 | NG1, PO4 |
| 2 | 824 | 0.79 | 0.82 | 88 | NG1, PO4 |
| 3 | 159 | 0.54 | 0.80 | 29 | empty |
| 4 | 213 | 0.53 | 0.77 | 29 | empty |
| 5 | 164 | 0.46 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1036 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2DKD · Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P4V2 · AlphaFold monomer V2.0 prediction for phosphoacetylglucosamine mutase (Q9P4V2) · a predicted model of the same protein · chain B 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 Q9P4V2
- Elsewhere: RCSB PDB 2DKD · PDBe 2DKD · UniProt Q9P4V2
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