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Crystal structure of glycerophosphodiester phosphodiesterase from thermococcus kodakarensis KOD1
Analyse Crystal structure of glycerophosphodiester phosphodiesterase from thermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OEC
- Type
- protein
- Length
- 992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphoryl diester phosphodiesterase
- EC
- 3.1.4.46
- UniProt
- Q5JGZ3
- Ligands
- MG
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycerophosphoryl diester phosphodiesterase (EC 3.1.4.46) | protein | 248 | 42% helix, 20% strand | Q5JGZ3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.73 | 0.78 | 81 | empty |
| 2 | 372 | 0.66 | 0.80 | 44 | empty |
| 3 | 181 | 0.65 | 0.84 | 26 | empty |
| 4 | 181 | 0.64 | 0.84 | 23 | empty |
| 5 | 197 | 0.63 | 0.82 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–D · 591 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 514 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 129 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 125 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OEC · Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus… · 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 Q5JGZ3
- Elsewhere: RCSB PDB 4OEC · PDBe 4OEC · UniProt Q5JGZ3
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