Research workbench
Crystal structure of D-galactose-6-phosphate isomerase in complex with D-psicose
Analyse Crystal structure of D-galactose-6-phosphate isomerase in complex with D-psicose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LFM
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-6-phosphate isomerase subunit a; Galactose-6-phosphate isomerase subunit B
- EC
- 5.3.1.26
- UniProt
- C7TGZ6, C7TGZ5
- Ligands
- PSJ
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Galactose-6-phosphate isomerase subunit a (EC 5.3.1.26) | protein | 142 | 49% helix, 18% strand | C7TGZ6 |
| B, D | Galactose-6-phosphate isomerase subunit B (EC 5.3.1.26) | protein | 172 | 47% helix, 15% strand | C7TGZ5 |
Ligands and binding sites
- PSJ · D-psicose · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.72 | 0.99 | 15 | empty |
| 2 | 110 | 0.63 | 0.88 | 23 | PSJ |
| 3 | 102 | 0.58 | 0.86 | 23 | PSJ |
| 4 | 206 | 0.49 | 0.76 | 29 | empty |
| 5 | 78 | 0.38 | 0.77 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2055 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2041 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 426 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 321 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4LFM · Crystal Structure of D-galactose-6-phosphate isomerase in complex with D-psicose · 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 C7TGZ6
- Every structure of UniProt C7TGZ5
- Elsewhere: RCSB PDB 4LFM · PDBe 4LFM · UniProt C7TGZ6 · UniProt C7TGZ5
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