MolNFT v1 · #93901 · protein
2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from bacteroides thetaiotaomicron in complex with transition state mimic
4HGO · Acylneuraminate cytidylyltransferase: “2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from bacteroides thetaiotaomicron in…”. X-ray diffraction, 3 ligands (VN4, KDN, MG), 5 pockets (best druggability 0.77).…
- PDB
- 4HGO
- Type
- protein
- Length
- 651 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylneuraminate cytidylyltransferase
- UniProt
- Q8A712
- Ligands
- VN4, KDN, MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acylneuraminate cytidylyltransferase | protein | 163 | 39% helix, 17% strand | Q8A712 |
| D | Acylneuraminate cytidylyltransferase | protein | 162 | 40% helix, 17% strand | Q8A712 |
Ligands and binding sites
- VN4 · oxido(dioxo)vanadium · ligand · 4 copies · chains A, B, C, D
- KDN · deamino-beta-neuraminic acid · sugar · 2 copies · chains A, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.77 | 0.79 | 128 | empty |
| 2 | 299 | 0.61 | 0.79 | 33 | MG, VN4, KDN |
| 3 | 291 | 0.60 | 0.79 | 32 | VN4, KDN |
| 4 | 240 | 0.57 | 0.78 | 28 | MG, VN4 |
| 5 | 207 | 0.52 | 0.77 | 26 | MG, VN4 |
Interfaces
6 interfaces between chains.
- A–B · 1243 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1218 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1202 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1202 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HGO · 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides… · the same entry in another collection · chain A against A, 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 D 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 4HGO · PDBe 4HGO · UniProt Q8A712
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