Research workbench
Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of zymomonas mobilis ZM4 with 3-phosphoglycerate
Analyse Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XSF
- Type
- protein
- Length
- 209 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KHG/KDPG aldolase
- EC
- 4.1.2.14
- UniProt
- Q00384
- Ligands
- 3PG, 3PY, PO4
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KHG/KDPG aldolase (EC 4.1.2.14) | protein | 209 | 43% helix, 18% strand | Q00384 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · chains A
- 3PY · 3-hydroxypyruvic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.32 | 0.77 | 14 | 3PY |
Compared structures
- 5XSF · Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00384 · AlphaFold monomer V2.0 prediction for KHG/KDPG aldolase (Q00384) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q00384
- Elsewhere: RCSB PDB 5XSF · PDBe 5XSF · UniProt Q00384
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