Research workbench
Mechanism of the class I kdpg aldolase
Analyse Mechanism of the class I kdpg aldolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WA3
- Type
- protein
- Length
- 1,211 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-3-deoxy-6-phosphogluconate aldolase
- EC
- 4.1.2.14
- UniProt
- Q9WXS1
- Ligands
- PYR, SO4
- Pockets
- 10 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | 2-keto-3-deoxy-6-phosphogluconate aldolase (EC 4.1.2.14) | protein | 202 | 51% helix, 17% strand | Q9WXS1 |
| C, F | 2-keto-3-deoxy-6-phosphogluconate aldolase (EC 4.1.2.14) | protein | 201 | 51% helix, 17% strand | Q9WXS1 |
| D | 2-keto-3-deoxy-6-phosphogluconate aldolase (EC 4.1.2.14) | protein | 203 | 50% helix, 17% strand | Q9WXS1 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.57 | 0.78 | 31 | empty |
| 2 | 211 | 0.57 | 0.79 | 23 | empty |
| 3 | 194 | 0.57 | 0.80 | 30 | SO4 |
| 4 | 169 | 0.54 | 0.80 | 28 | SO4 |
| 5 | 161 | 0.53 | 0.80 | 28 | SO4 |
Interfaces
6 interfaces between chains.
- D–F · 662 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 642 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 630 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 626 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 disulfide (covalent ligand, disulfide).
Compared structures
- 1WA3 · Mechanism of the Class I KDPG aldolase · 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 Q9WXS1
- Elsewhere: RCSB PDB 1WA3 · PDBe 1WA3 · UniProt Q9WXS1
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