Research workbench
A quantum half-site enzyme
Analyse A quantum half-site enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LU5
- Type
- protein
- Length
- 773 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoheptose isomerase
- EC
- 5.3.1.28
- UniProt
- A0A095TT41
- Ligands
- M7P, NA, MG
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Phosphoheptose isomerase (EC 5.3.1.28) | protein | 193 | 60% helix, 11% strand | A0A095TT41 |
| D | Phosphoheptose isomerase (EC 5.3.1.28) | protein | 194 | 59% helix, 11% strand | A0A095TT41 |
Ligands and binding sites
- M7P · 7-O-phosphono-D-glycero-alpha-D-manno-heptopyranose · ligand · 4 copies · chains A, B, D, C
- NA · Sodium ion · metal
- MG · Magnesium ion · metal
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, D, C
- GOL · Glycerol · additive · 4 copies · chains B
- PGE · Triethylene glycol · additive · 3 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
- ACT · Acetate ion · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.73 | 0.98 | 23 | empty |
| 2 | 52 | 0.71 | 0.98 | 21 | empty |
| 3 | 241 | 0.62 | 0.81 | 41 | M7P, NA |
| 4 | 160 | 0.61 | 0.84 | 28 | M7P |
| 5 | 174 | 0.60 | 0.83 | 27 | M7P |
Interfaces
6 interfaces between chains.
- A–D · 1699 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1689 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1217 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1217 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 701 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5LU5 · A quantum half-site enzyme · 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 A0A095TT41
- Elsewhere: RCSB PDB 5LU5 · PDBe 5LU5 · UniProt A0A095TT41
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