Research workbench
Crystal structure of E56A/K67A mutant of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron
Analyse Crystal structure of E56A/K67A mutant of 2-keto-3-deoxy-D-glycero-D-galactononon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HGR
- Type
- protein
- Length
- 1,302 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Bacteroides thetaiotaomicron
- Molecule
- Acylneuraminate cytidylyltransferase
- UniProt
- Q8A712
- Ligands
- MG
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.05 · 5 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Acylneuraminate cytidylyltransferase | protein | 163 | 39% helix, 19% strand | Q8A712 |
| B, D | Acylneuraminate cytidylyltransferase | protein | 163 | 39% helix, 17% strand | Q8A712 |
| C | Acylneuraminate cytidylyltransferase | protein | 162 | 39% helix, 18% strand | Q8A712 |
| E | Acylneuraminate cytidylyltransferase | protein | 164 | 37% helix, 17% strand | Q8A712 |
| F, H | Acylneuraminate cytidylyltransferase | protein | 162 | 39% helix, 17% strand | Q8A712 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.84 | 0.89 | 106 | empty |
| 2 | 443 | 0.83 | 0.90 | 65 | empty |
| 3 | 523 | 0.82 | 0.88 | 67 | empty |
| 4 | 370 | 0.59 | 0.76 | 39 | MG |
| 5 | 338 | 0.57 | 0.76 | 37 | MG |
Interfaces
20 interfaces between chains.
- B–D · 1276 Ų buried · 17 hydrogen bonds · protein-protein
- F–H · 1258 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1212 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1200 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1169 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
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 Q8A712
- Elsewhere: RCSB PDB 4HGR · PDBe 4HGR · UniProt Q8A712
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.