MolNFT v1 · #153645 · protein
Crystal structure of N-acetylglucosamine-6-phosphate deacetylase from pasteurella multocida
6JKU: “Crystal structure of N-acetylglucosamine-6-phosphate deacetylase from pasteurella multocida”. X-ray diffraction, 3 ligands (ZN, NA, PO4), 10 pockets (best druggability 0.74). MolNFT v1 #153645 on GenesisL1: 3D structure, binding…
- PDB
- 6JKU
- Type
- protein
- Length
- 1,529 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-6-phosphate deacetylase
- UniProt
- A0A1E3XI56
- Ligands
- ZN, NA, PO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetylglucosamine-6-phosphate deacetylase | protein | 385 | 30% helix, 29% strand | A0A1E3XI56 |
| C | N-acetylglucosamine-6-phosphate deacetylase | protein | 380 | 29% helix, 29% strand | A0A1E3XI56 |
| D | N-acetylglucosamine-6-phosphate deacetylase | protein | 379 | 31% helix, 28% strand | A0A1E3XI56 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 15 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.74 | 0.99 | 21 | empty |
| 2 | 67 | 0.74 | 0.98 | 20 | empty |
| 3 | 128 | 0.56 | 0.83 | 28 | PO4, ZN, EDO |
| 4 | 195 | 0.54 | 0.78 | 25 | empty |
| 5 | 131 | 0.54 | 0.82 | 29 | PO4 |
Interfaces
4 interfaces between chains.
- C–D · 1018 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 980 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 496 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6JKU · Crystal structure of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella… · the same entry in another collection · chain A against A, 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 A0A1E3XI56
- Elsewhere: RCSB PDB 6JKU · PDBe 6JKU · UniProt A0A1E3XI56
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