MolNFT v1 · #110516 · protein
Transaldolase variant E60Q/F132Y from T. acidophilum in complex with dha schiff base and G3P
4XZ9 · Probable transaldolase: “Transaldolase variant E60Q/F132Y from T. acidophilum in complex with dha schiff base and G3P”. X-ray diffraction, 1 ligand (G3P), 10 pockets (best druggability 0.60). MolNFT v1 #110516 on GenesisL1: 3D…
- PDB
- 4XZ9
- Type
- protein
- Length
- 1,102 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
- Ligands
- G3P
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable transaldolase (EC 2.2.1.2) | protein | 217 | 53% helix, 18% strand | Q9HKI3 |
| C, D | Probable transaldolase (EC 2.2.1.2) | protein | 223 | 51% helix, 17% strand | Q9HKI3 |
| E | Probable transaldolase (EC 2.2.1.2) | protein | 222 | 51% helix, 17% strand | Q9HKI3 |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · 2 copies · chains B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 4 copies · chains B, C, E
- PDO · 1,3-propandiol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.60 | 0.81 | 34 | empty |
| 2 | 164 | 0.51 | 0.78 | 26 | empty |
| 3 | 62 | 0.49 | 0.85 | 15 | empty |
| 4 | 140 | 0.45 | 0.76 | 23 | empty |
| 5 | 59 | 0.43 | 0.81 | 11 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1926 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1821 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1611 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1497 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1353 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4XZ9 · Transaldolase variant E60Q/F132Y from T. acidophilum in complex with DHA Schiff base and… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HKI3 · AlphaFold monomer V2.0 prediction for probable transaldolase (Q9HKI3) · a predicted model of the same protein · chain C 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 Q9HKI3
- Elsewhere: RCSB PDB 4XZ9 · PDBe 4XZ9 · UniProt Q9HKI3
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