Research workbench
Structure of the spx domain of chaetomium thermophilum glycerophosphodiester phosphodiesterase 1 in complex with inositol hexakisphosphate (INSP6)
Analyse Structure of the spx domain of chaetomium thermophilum glycerophosphodiester… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IJJ
- Type
- protein
- Length
- 332 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spx domain
- EC
- 3.1.4.46
- UniProt
- G0RY29
- Ligands
- IHP
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spx domain (EC 3.1.4.46) | protein | 175 | 80% helix, 0% strand | G0RY29 |
| B | Spx domain (EC 3.1.4.46) | protein | 157 | 84% helix, 0% strand | G0RY29 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.81 | 0.82 | 100 | EDO |
Interfaces
1 interface between chains.
- A–B · 631 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5IJJ · Structure of the SPX domain of Chaetomium thermophilum Glycerophosphodiester… · 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 G0RY29
- Elsewhere: RCSB PDB 5IJJ · PDBe 5IJJ · UniProt G0RY29
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