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Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes GLU164GLN mutant in complex with fbp
Analyse Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes GLU164GLN mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F2G
- Type
- protein
- Length
- 1,295 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
- P6F, 13P, CA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 323 | 48% helix, 15% strand | P63705 |
| B | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 325 | 49% helix, 15% strand | P63705 |
| D | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 324 | 49% helix, 15% strand | P63705 |
Ligands and binding sites
- P6F · 1,6-di-O-phosphono-D-fructose · ligand · chains A
- 13P · 1,3-dihydroxyacetonephosphate · ligand · chains B
- CA · Calcium ion · metal · 5 copies · chains B, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.79 | 0.81 | 93 | CA |
| 2 | 400 | 0.71 | 0.82 | 50 | P6F |
| 3 | 403 | 0.69 | 0.81 | 45 | 13P |
| 4 | 398 | 0.68 | 0.80 | 46 | empty |
| 5 | 439 | 0.67 | 0.79 | 48 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1040 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1034 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 644 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 143 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5F2G · Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes Glu164Gln mutant in… · 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 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 5F2G · PDBe 5F2G · UniProt P63705
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