Research workbench
Dihydroxyacetone phosphate carbanion intermediate in tagatose-1,6- bisphosphate aldolase from streptococcus pyogenes
Analyse Dihydroxyacetone phosphate carbanion intermediate in tagatose-1,6- bisphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MHG
- Type
- protein
- Length
- 1,292 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
- 13P, CA
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 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 | 323 | 48% helix, 15% strand | P63705 |
| B | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 323 | 48% helix, 15% strand | P63705 |
| C | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 322 | 48% helix, 16% 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
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.78 | 0.80 | 80 | CA |
| 2 | 413 | 0.71 | 0.82 | 57 | 13P |
| 3 | 393 | 0.70 | 0.82 | 51 | 13P |
| 4 | 362 | 0.68 | 0.82 | 48 | 13P |
| 5 | 364 | 0.68 | 0.81 | 50 | 13P |
Interfaces
4 interfaces between chains.
- A–B · 1045 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1039 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 614 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 146 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3MHG · Dihydroxyacetone phosphate carbanion intermediate in tagatose-1,6-bisphosphate aldolase… · the same entry in another collection · chain D against D, 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 B 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 3MHG · PDBe 3MHG · UniProt P63705
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