Research workbench
Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes GLU163GLN mutant
Analyse Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes GLU163GLN mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F2I
- Type
- protein
- Length
- 1,298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tagatose 1,6-diphosphate aldolase 2
- EC
- 4.1.2.40
- UniProt
- P63705
- Ligands
- CA
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 324 | 50% helix, 15% strand | P63705 |
| B, C | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 324 | 49% helix, 15% strand | P63705 |
| D | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 326 | 48% helix, 15% strand | P63705 |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, A, C, D
- ACT · Acetate ion · additive · chains A
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 | 1119 | 0.80 | 0.82 | 85 | ACT, CA, GOL |
| 2 | 586 | 0.72 | 0.80 | 65 | empty |
| 3 | 495 | 0.70 | 0.80 | 53 | empty |
| 4 | 477 | 0.70 | 0.80 | 50 | empty |
| 5 | 485 | 0.69 | 0.79 | 54 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1068 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1052 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 679 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 146 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5F2I · Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes Glu163Gln mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P63705 · AlphaFold monomer V2.0 prediction for tagatose 1,6-diphosphate aldolase 2 (P63705) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P63705
- Elsewhere: RCSB PDB 5F2I · PDBe 5F2I · UniProt P63705
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.