Research workbench
1.9A structure of glycerophoshphodiesterase (gpdq) from enterobacter aerogenes
Analyse 1.9A structure of glycerophoshphodiesterase (gpdq) from enterobacter aerogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D03
- Type
- protein
- Length
- 1,632 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphohydrolase
- EC
- 3.1.4.46
- UniProt
- Q6XBH1
- Ligands
- CO
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Phosphohydrolase (EC 3.1.4.46) | protein | 274 | 26% helix, 26% strand | Q6XBH1 |
| B, C, D, E | Phosphohydrolase (EC 3.1.4.46) | protein | 271 | 26% helix, 27% strand | Q6XBH1 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.82 | 0.93 | 56 | empty |
| 2 | 468 | 0.82 | 0.89 | 73 | empty |
| 3 | 298 | 0.82 | 0.92 | 55 | empty |
| 4 | 465 | 0.81 | 0.88 | 73 | empty |
| 5 | 191 | 0.78 | 0.93 | 41 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2854 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 2834 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 2649 Ų buried · 40 hydrogen bonds · protein-protein
- A–F · 903 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 744 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3D03 · 1.9A structure of Glycerophoshphodiesterase (GpdQ) 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 3D03 · PDBe 3D03 · UniProt Q6XBH1
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