MolNFT v1 · #71547 · protein
Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes
3MHF · Tagatose 1,6-diphosphate aldolase 2: “Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability 0.79). MolNFT v1 #71547 on GenesisL1: 3D structure, binding sites…
- PDB
- 3MHF
- 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
- CA
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 322 | 49% helix, 15% strand | P63705 |
| C | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 324 | 48% helix, 15% strand | P63705 |
| D | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 324 | 46% helix, 15% strand | P63705 |
Ligands and binding sites
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.79 | 0.81 | 88 | CA |
| 2 | 449 | 0.67 | 0.79 | 54 | empty |
| 3 | 396 | 0.65 | 0.79 | 49 | empty |
| 4 | 405 | 0.65 | 0.79 | 46 | empty |
| 5 | 407 | 0.64 | 0.78 | 48 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1050 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1036 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 654 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 142 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3MHF · Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes · 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 3MHF · PDBe 3MHF · UniProt P63705
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