MolNFT v1 · #56714 · protein
Malonate-bound structure of the glycerophosphodiesterase from enterobacter aerogenes (gpdq) collected at 1.280 ångström
2ZOA · Phosphohydrolase: “Malonate-bound structure of the glycerophosphodiesterase from enterobacter aerogenes (gpdq) collected at…”. X-ray diffraction, 1 ligand (FE2), 7 pockets (best druggability 0.75). MolNFT v1 #56714 on GenesisL1: 3D…
- PDB
- 2ZOA
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphohydrolase
- EC
- 3.1.4.46
- UniProt
- Q6XBH1
- Ligands
- FE2
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphohydrolase (EC 3.1.4.46) | protein | 271 | 25% helix, 27% strand | Q6XBH1 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B
- MLI · Malonate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.75 | 0.82 | 66 | empty |
| 2 | 187 | 0.57 | 0.81 | 35 | MLI |
| 3 | 167 | 0.56 | 0.81 | 27 | MLI |
| 4 | 106 | 0.39 | 0.76 | 15 | empty |
| 5 | 74 | 0.35 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2699 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2ZOA · Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes… · 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 Q6XBH1
- Elsewhere: RCSB PDB 2ZOA · PDBe 2ZOA · UniProt Q6XBH1
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