Research workbench
Structure-function analysis of 2-keto-3-deoxy-D-glycero-D-galacto- nononate-9-phosphate (kdn) phosphatase defines a new clad within the type C0 had subfamily
Analyse Structure-function analysis of 2-keto-3-deoxy-D-glycero-D-galacto… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E8M
- Type
- protein
- Length
- 656 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylneuraminate cytidylyltransferase
- UniProt
- Q8A712
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acylneuraminate cytidylyltransferase | protein | 164 | 38% helix, 17% strand | Q8A712 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 6 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains 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 | 981 | 0.79 | 0.81 | 127 | CL, PG4, EDO |
| 2 | 295 | 0.60 | 0.78 | 33 | ACY, MG, CL |
| 3 | 289 | 0.59 | 0.78 | 35 | ACY, CL, EDO |
| 4 | 309 | 0.59 | 0.77 | 34 | MG, CL, ACY |
| 5 | 265 | 0.58 | 0.78 | 32 | MG, CL, ACY |
Interfaces
6 interfaces between chains.
- B–D · 1259 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1247 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1214 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1211 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3E8M · Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate… · 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 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 3E8M · PDBe 3E8M · UniProt Q8A712
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