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The structure of an oleispira antarctica phosphodiesterase OLEI02445 in complex with the product sn-glycerol-3-phosphate
Analyse The structure of an oleispira antarctica phosphodiesterase OLEI02445 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QVQ
- Type
- protein
- Length
- 998 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase OLEI02445
- EC
- 3.1.4.2
- Ligands
- G3P, MG, NA, NI, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase OLEI02445 (EC 3.1.4.2) | protein | 251 | 39% helix, 19% strand | — |
| B | Phosphodiesterase OLEI02445 (EC 3.1.4.2) | protein | 250 | 38% helix, 19% strand | — |
| C | Phosphodiesterase OLEI02445 (EC 3.1.4.2) | protein | 250 | 39% helix, 19% strand | — |
| D | Phosphodiesterase OLEI02445 (EC 3.1.4.2) | protein | 247 | 38% helix, 19% strand | — |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 13 copies · chains A, B, C, D
- NA · Sodium ion · metal · 7 copies · chains A, D, B, C
- NI · Nickel (II) ion · metal · chains A, B
- CL · Chloride ion · ion · 18 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.75 | 0.79 | 78 | G3P, MG |
| 2 | 439 | 0.60 | 0.75 | 48 | PEG, CL |
| 3 | 328 | 0.55 | 0.75 | 40 | CL |
| 4 | 273 | 0.53 | 0.75 | 31 | CL |
| 5 | 143 | 0.42 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1175 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 195 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3QVQ · The structure of an Oleispira antarctica phosphodiesterase OLEI02445 in complex with the… · 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
- Elsewhere: RCSB PDB 3QVQ · PDBe 3QVQ
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