Research workbench
Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes in complex with competitive inhibitor talitol-1,6-bisphosphate
Analyse Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F2L
- Type
- protein
- Length
- 1,300 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
- M2P, CA, CL
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 48% 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 | 49% helix, 15% strand | P63705 |
| C | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 326 | 48% helix, 15% strand | P63705 |
| B, D | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 325 | 49% helix, 15% strand | P63705 |
Ligands and binding sites
- M2P · D-mannitol-1,6-diphosphate · ligand · chains A
- CA · Calcium ion · metal · 7 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains C, B, D
- ACT · Acetate ion · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.82 | 0.83 | 90 | CA, ACT |
| 2 | 380 | 0.72 | 0.84 | 51 | M2P |
| 3 | 487 | 0.70 | 0.80 | 56 | CL |
| 4 | 442 | 0.70 | 0.81 | 54 | CL |
| 5 | 285 | 0.64 | 0.81 | 43 | CL |
Interfaces
4 interfaces between chains.
- C–B · 1050 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1039 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 143 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5F2L · Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with… · the same entry in another collection · chain C against C, 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 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 P63705
- Elsewhere: RCSB PDB 5F2L · PDBe 5F2L · UniProt P63705
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