Research workbench
Crystal structure of a three sites mutantion of fsaa complexed with ha and product
Analyse Crystal structure of a three sites mutantion of fsaa complexed with ha and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZOL
- Type
- protein
- Length
- 2,212 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-6-phosphate aldolase 1
- EC
- 4.1.2.-
- UniProt
- P78055
- Ligands
- 4Y8, LW2, LW1, SO4, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Fructose-6-phosphate aldolase 1 (EC 4.1.2.-) | protein | 222 | 53% helix, 17% strand | P78055 |
| B, C, D, E, F, H, I, J | Fructose-6-phosphate aldolase 1 (EC 4.1.2.-) | protein | 221 | 53% helix, 17% strand | P78055 |
Ligands and binding sites
- 4Y8 · 1-hydroxypropan-2-one · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- LW2 · (3S,4S)-3,4-dihydroxy-4-(thiophen-2-yl)butan-2-one · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I, J
- LW1 · thiophene-2-carbaldehyde · ligand · chains G
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, D, E, F, G, H, I, J
- CL · Chloride ion · ion · 4 copies · chains A, C, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.78 | 0.83 | 81 | 4Y8, LW1 |
| 2 | 859 | 0.77 | 0.80 | 116 | 4Y8, LW2 |
| 3 | 737 | 0.76 | 0.81 | 93 | 4Y8, LW2 |
| 4 | 477 | 0.74 | 0.83 | 66 | 4Y8, LW2 |
| 5 | 366 | 0.69 | 0.82 | 50 | 4Y8, LW2 |
Interfaces
20 interfaces between chains.
- A–E · 1670 Ų buried · 7 hydrogen bonds · protein-protein
- I–J · 1662 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1661 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1657 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 1657 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 5ZOL · Crystal structure of a three sites mutantion of FSAA complexed with HA and product · the same entry in another collection · chain J against J, TM-score 1.00
- P78055 · AlphaFold monomer V2.0 prediction for fructose-6-phosphate aldolase 1 (P78055) · a predicted model of the same protein · chain E 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 P78055
- Elsewhere: RCSB PDB 5ZOL · PDBe 5ZOL · UniProt P78055
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