MolNFT v1 · #118465 · protein
Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes in complex with competitive inhibitor hexitol-1,6-bisphosphate
5F2M · Tagatose 1,6-diphosphate aldolase 2: “Tagatose-1,6-bisphosphate aldolase from streptococcus pyogenes in complex with competitive inhibitor…”. X-ray diffraction, 2 ligands (M2P, CA), 13 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5F2M
- 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
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 49% 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 | 48% helix, 15% strand | P63705 |
| B | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 324 | 48% helix, 15% strand | P63705 |
| C, D | Tagatose 1,6-diphosphate aldolase 2 (EC 4.1.2.40) | protein | 326 | 49% helix, 14% strand | P63705 |
Ligands and binding sites
- M2P · D-mannitol-1,6-diphosphate · ligand · chains A
- CA · Calcium ion · metal · 10 copies · chains A, B, C, 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 | 1125 | 0.80 | 0.81 | 77 | CA |
| 2 | 487 | 0.72 | 0.81 | 63 | empty |
| 3 | 446 | 0.71 | 0.81 | 60 | empty |
| 4 | 372 | 0.70 | 0.82 | 46 | M2P |
| 5 | 449 | 0.69 | 0.80 | 62 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1048 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1031 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 705 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5F2M · Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with… · 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 5F2M · PDBe 5F2M · UniProt P63705
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