Research workbench
Transaldolase variant LYS86ALA from thermoplasma acidophilum in complex with glycerol and citrate
Analyse Transaldolase variant LYS86ALA from thermoplasma acidophilum in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S1W
- Type
- protein
- Length
- 1,115 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transaldolase
- EC
- 2.2.1.2
- UniProt
- Q9HKI3
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Probable transaldolase (EC 2.2.1.2) | protein | 223 | 52% helix, 17% strand | Q9HKI3 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E
- FLC · Citrate anion · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.47 | 0.80 | 30 | GOL, FLC |
| 2 | 106 | 0.47 | 0.80 | 30 | GOL, FLC |
| 3 | 101 | 0.45 | 0.79 | 31 | GOL, FLC |
| 4 | 80 | 0.33 | 0.74 | 17 | FLC |
| 5 | 58 | 0.30 | 0.75 | 12 | FLC |
Interfaces
5 interfaces between chains.
- B–C · 1850 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1841 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1835 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1796 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1746 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3S1W · Transaldolase variant Lys86Ala from Thermoplasma acidophilum in complex with glycerol and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HKI3 · AlphaFold monomer V2.0 prediction for probable transaldolase (Q9HKI3) · 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 Q9HKI3
- Elsewhere: RCSB PDB 3S1W · PDBe 3S1W · UniProt Q9HKI3
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