MolNFT v1 · #55820 · protein
Crystal structure analysis of the 4-hydroxy-2-oxoglutarate ALDOLASE/2- deydro-3-deoxyphosphogluconate aldolase from TTHB1
2YW3 · 4-hydroxy-2-oxoglutarate ALDOLASE/2-deydro-3…: “Crystal structure analysis of the 4-hydroxy-2-oxoglutarate ALDOLASE/2- deydro-3-deoxyphosphogluconate…”. X-ray diffraction, 1 ligand (PO4), 14 pockets (best druggability 0.61). MolNFT…
- PDB
- 2YW3
- Type
- protein
- Length
- 1,187 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-2-oxoglutarate ALDOLASE/2-deydro-3- deoxyphosphogluconate aldolase
- EC
- 4.1.2.14
- UniProt
- Q53W90
- Ligands
- PO4
- Pockets
- 14 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-2-oxoglutarate ALDOLASE/2-deydro-3- deoxyphosphogluconate aldolase (EC 4.1.2.14) | protein | 195 | 46% helix, 19% strand | Q53W90 |
| B, C | 4-hydroxy-2-oxoglutarate ALDOLASE/2-deydro-3- deoxyphosphogluconate aldolase (EC 4.1.2.14) | protein | 197 | 46% helix, 19% strand | Q53W90 |
| D | 4-hydroxy-2-oxoglutarate ALDOLASE/2-deydro-3- deoxyphosphogluconate aldolase (EC 4.1.2.14) | protein | 199 | 46% helix, 18% strand | Q53W90 |
| E | 4-hydroxy-2-oxoglutarate ALDOLASE/2-deydro-3- deoxyphosphogluconate aldolase (EC 4.1.2.14) | protein | 200 | 47% helix, 18% strand | Q53W90 |
| F | 4-hydroxy-2-oxoglutarate ALDOLASE/2-deydro-3- deoxyphosphogluconate aldolase (EC 4.1.2.14) | protein | 199 | 46% helix, 18% strand | Q53W90 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 17 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.61 | 0.81 | 42 | PO4 |
| 2 | 238 | 0.60 | 0.80 | 41 | PO4 |
| 3 | 470 | 0.58 | 0.73 | 70 | empty |
| 4 | 194 | 0.56 | 0.80 | 38 | PO4 |
| 5 | 425 | 0.56 | 0.73 | 52 | empty |
Interfaces
9 interfaces between chains.
- A–C · 770 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 768 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 761 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 759 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 735 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2YW3 · Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate… · the same entry in another collection · 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 Q53W90
- Elsewhere: RCSB PDB 2YW3 · PDBe 2YW3 · UniProt Q53W90
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.