Research workbench
Crystal structure of yage, a kdg aldolase protein in complex with 2- keto-3-deoxy gluconate
Analyse Crystal structure of yage, a kdg aldolase protein in complex with 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ONV
- 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
- KDG
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 11% 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, 11% strand | P75682 |
Ligands and binding sites
- KDG · 2-keto-3-deoxygluconate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, D, C
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.70 | 0.97 | 21 | KDG |
| 2 | 141 | 0.69 | 0.90 | 37 | empty |
| 3 | 58 | 0.69 | 0.96 | 22 | KDG |
| 4 | 172 | 0.69 | 0.88 | 39 | GOL |
| 5 | 58 | 0.68 | 0.95 | 20 | KDG |
Interfaces
4 interfaces between chains.
- C–D · 1719 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1706 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 976 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 960 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4ONV · Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate · 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 4ONV · PDBe 4ONV · UniProt P75682
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