Research workbench
Crystal structure of the N-acetylmannosamine kinase domain of human gne protein
Analyse Crystal structure of the N-acetylmannosamine kinase domain of human gne protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EO3
- Type
- protein
- Length
- 857 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase
- EC
- 5.1.3.14, 2.7.1.60
- UniProt
- Q9Y223
- Ligands
- ZN, UNX
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase (EC 5.1.3.14, 2.7.1.60) | protein | 288 | 44% helix, 22% strand | Q9Y223 |
| B | Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase (EC 5.1.3.14, 2.7.1.60) | protein | 283 | 44% helix, 20% strand | Q9Y223 |
| C | Bifunctional udp-N-acetylglucosamine 2-EPIMERASE/N- acetylmannosamine kinase (EC 5.1.3.14, 2.7.1.60) | protein | 286 | 43% helix, 22% strand | Q9Y223 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- UNX · Unknown atom or ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.47 | 0.75 | 44 | empty |
| 2 | 204 | 0.46 | 0.75 | 33 | UNX |
| 3 | 63 | 0.44 | 0.83 | 17 | empty |
| 4 | 175 | 0.44 | 0.75 | 34 | UNX |
Interfaces
3 interfaces between chains.
- A–B · 116 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3EO3 · Crystal structure of the N-acetylmannosamine kinase domain of human GNE protein · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y223 · AlphaFold monomer V2.0 prediction for bifunctional udp-N- acetylglucosamine… · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q9Y223
- Elsewhere: RCSB PDB 3EO3 · PDBe 3EO3 · UniProt Q9Y223
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