Research workbench
Crystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919 from silicibacter pomeroyi (YP_168127.1) from silicibacter pomeroyi dss-3 at 2.30 a resolution
Analyse Crystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I7D
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar phosphate isomerase
- UniProt
- Q5LPC9
- Ligands
- CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar phosphate isomerase | protein | 157 | 10% helix, 43% strand | Q5LPC9 |
| B | Sugar phosphate isomerase | protein | 158 | 9% helix, 44% strand | Q5LPC9 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.77 | 0.85 | 41 | CAC |
| 2 | 610 | 0.77 | 0.83 | 50 | CAC, ACT |
| 3 | 91 | 0.36 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1429 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3I7D · Crystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919 from… · 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 Q5LPC9
- Elsewhere: RCSB PDB 3I7D · PDBe 3I7D · UniProt Q5LPC9
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