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A putative tagatose 1,6-diphosphate aldolase from Streptococcus pyogenes
Analyse A putative tagatose 1,6-diphosphate aldolase from Streptococcus pyogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JRK
- Type
- protein
- Length
- 2,572 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.97
- Source
- Streptococcus pyogenes serotype M1
- Molecule
- Tagatose 1,6-diphosphate aldolase 2
- EC
- 4.1.2.40
- UniProt
- P63705
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.97 · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 322 | 48% helix, 16% strand | P63705 |
| F | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 321 | 49% helix, 15% strand | P63705 |
| H | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 319 | 50% helix, 15% strand | P63705 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.77 | 0.79 | 101 | empty |
| 2 | 519 | 0.73 | 0.82 | 58 | GOL |
| 3 | 482 | 0.72 | 0.81 | 57 | empty |
| 4 | 602 | 0.72 | 0.79 | 59 | GOL |
| 5 | 492 | 0.71 | 0.81 | 47 | empty |
Interfaces
9 interfaces between chains.
- A–H · 1064 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 1058 Ų buried · 30 hydrogen bonds · protein-protein
- C–G · 1052 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 944 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 944 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 modified (engineered).
Compared structures
- 3JRK · A putative tagatose 1,6-diphosphate aldolase from streptococcus pyogenes · the same entry in another collection · chain H against H, 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 H 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 3JRK · PDBe 3JRK · UniProt P63705
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