Research workbench
Crystal structure of E56A mutant of 2-keto-3-deoxy-D-glycero-D- galactonononate-9-phosphate phosphohydrolase from bacteroides thetaiotaomicron
Analyse Crystal structure of E56A mutant of 2-keto-3-deoxy-D-glycero-D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HGQ
- Type
- protein
- Length
- 1,312 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylneuraminate cytidylyltransferase
- UniProt
- Q8A712
- Ligands
- MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Acylneuraminate cytidylyltransferase | protein | 164 | 38% helix, 18% 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
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.76 | 0.79 | 128 | empty |
| 2 | 1184 | 0.75 | 0.78 | 130 | empty |
| 3 | 921 | 0.75 | 0.78 | 63 | MG |
| 4 | 810 | 0.71 | 0.77 | 63 | MG |
| 5 | 168 | 0.63 | 0.84 | 25 | empty |
Interfaces
15 interfaces between chains.
- A–C · 1251 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1242 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1227 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 1218 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1216 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4HGQ · Crystal structure of E56A mutant of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8A712 · AlphaFold monomer V2.0 prediction for 2-keto-3-deoxy-D-glycero-D… · a predicted model of the same protein · 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 Q8A712
- Elsewhere: RCSB PDB 4HGQ · PDBe 4HGQ · UniProt Q8A712
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