Research workbench
Malonate-bound structure of the glycerophosphodiesterase from enterobacter aerogenes (gpdq) and characterization of the native FE2+ metal ion preference
Analyse Malonate-bound structure of the glycerophosphodiesterase from enterobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZO9
- 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 0.76
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | 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 B, C
- MLI · Malonate ion · additive · 2 copies · chains B, C
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 | 558 | 0.76 | 0.83 | 68 | empty |
| 2 | 107 | 0.57 | 0.85 | 19 | MLI |
| 3 | 158 | 0.57 | 0.82 | 25 | MLI |
| 4 | 109 | 0.42 | 0.77 | 18 | empty |
| 5 | 96 | 0.40 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- B–C · 2729 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2ZO9 · Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes… · the same entry in another collection · chain B against B, 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 2ZO9 · PDBe 2ZO9 · UniProt Q6XBH1
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