Research workbench
Structural genomics, crystal structure of glycerophosphoryl diester phosphodiesterase from E. COLI
Analyse Structural genomics, crystal structure of glycerophosphoryl diester… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T8Q
- Type
- protein
- Length
- 1,312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphoryl diester phosphodiesterase, periplasmic
- EC
- 3.1.4.46
- UniProt
- P09394
- Ligands
- MG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glycerophosphoryl diester phosphodiesterase, periplasmic (EC 3.1.4.46) | protein | 328 | 33% helix, 21% strand | P09394 |
| B | Glycerophosphoryl diester phosphodiesterase, periplasmic (EC 3.1.4.46) | protein | 329 | 33% helix, 22% strand | P09394 |
| D | Glycerophosphoryl diester phosphodiesterase, periplasmic (EC 3.1.4.46) | protein | 327 | 33% helix, 21% strand | P09394 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.77 | 0.97 | 19 | empty |
| 2 | 171 | 0.73 | 0.90 | 28 | empty |
| 3 | 966 | 0.73 | 0.76 | 99 | MG, GOL |
| 4 | 578 | 0.67 | 0.77 | 52 | GOL |
| 5 | 388 | 0.63 | 0.78 | 41 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 1225 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1178 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 781 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 1T8Q · Structural genomics, Crystal structure of Glycerophosphoryl diester phosphodiesterase… · the same entry in another collection · chain A against A, TM-score 1.00
- P09394 · AlphaFold monomer V2.0 prediction for glycerophosphodiester phosphodiesterase… · a predicted model of the same protein · chain B 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 P09394
- Elsewhere: RCSB PDB 1T8Q · PDBe 1T8Q · UniProt P09394
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