MolNFT v1 · #103869 · protein
Crystal structure of yage, a kdg aldolase protein in complex with magnesium cation coordinated L-glyceraldehyde
4PTN · Probable 2-keto-3-deoxy-galactonate aldolase yage: “Crystal structure of yage, a kdg aldolase protein in complex with magnesium cation coordinated…”. X-ray diffraction, 3 ligands (GXV, PYR, MG), 11 pockets (best druggability 0.72).…
- PDB
- 4PTN
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 2-keto-3-deoxy-galactonate aldolase yage
- EC
- 4.1.2.-
- UniProt
- P75682
- Ligands
- GXV, PYR, MG
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable 2-keto-3-deoxy-galactonate aldolase yage (EC 4.1.2.-) | protein | 298 | 52% helix, 12% strand | P75682 |
Ligands and binding sites
- GXV · L-glyceraldehyde · ligand · 4 copies · chains A, B, C, D
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, B, D
- GOL · Glycerol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.72 | 0.91 | 37 | empty |
| 2 | 61 | 0.70 | 0.96 | 20 | GXV, MG |
| 3 | 61 | 0.70 | 0.97 | 23 | GXV, MG |
| 4 | 196 | 0.69 | 0.87 | 39 | empty |
| 5 | 57 | 0.68 | 0.96 | 18 | GXV, MG |
Interfaces
4 interfaces between chains.
- A–B · 1696 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1690 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 965 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 946 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4PTN · Crystal Structure of YagE, a KDG aldolase protein in complex with Magnesium cation… · the same entry in another collection · chain A against A, TM-score 1.00
- P75682 · AlphaFold monomer V2.0 prediction for putative 2-dehydro-3-deoxy-D- gluconate aldolase… · 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 P75682
- Elsewhere: RCSB PDB 4PTN · PDBe 4PTN · UniProt P75682
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.