MolNFT v1 · #51368 · protein
Apo class II aldolase hpch
2V5J · 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase: “Apo class II aldolase hpch”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.62). MolNFT v1 #51368 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2V5J
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
- EC
- 4.1.2.-
- UniProt
- Q47098
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.-) | protein | 268 | 49% helix, 16% strand | Q47098 |
| B | 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.-) | protein | 261 | 48% helix, 16% strand | Q47098 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.62 | 0.85 | 29 | GOL |
| 2 | 155 | 0.62 | 0.85 | 30 | GOL |
| 3 | 143 | 0.41 | 0.74 | 30 | empty |
| 4 | 150 | 0.40 | 0.73 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1631 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 Q47098
- Elsewhere: RCSB PDB 2V5J · PDBe 2V5J · UniProt Q47098
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