Research workbench
Transaldolase variant T30D from T. acidophilum in complex with D- fructose 6-phosphate schiff-base intermediate
Analyse Transaldolase variant T30D from T. acidophilum in complex with D- fructose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YRT
- Type
- protein
- Length
- 1,097 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaldolase
- EC
- 2.2.1.2
- UniProt
- Q9HKI3
- Ligands
- F6R
- Pockets
- 10 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Transaldolase (EC 2.2.1.2) | protein | 217 | 53% helix, 18% strand | Q9HKI3 |
| C, D | Transaldolase (EC 2.2.1.2) | protein | 223 | 51% helix, 17% strand | Q9HKI3 |
Ligands and binding sites
- F6R · Fructose -6-phosphate · ligand · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.47 | 0.79 | 17 | empty |
| 2 | 127 | 0.46 | 0.78 | 25 | F6R |
| 3 | 113 | 0.46 | 0.78 | 18 | empty |
| 4 | 111 | 0.45 | 0.79 | 30 | F6R |
| 5 | 54 | 0.45 | 0.84 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1876 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1832 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1563 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1553 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1515 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6YRT · Transaldolase variant T30D from T. acidophilum in complex with D-fructose 6-phosphate… · the same entry in another collection · chain B against B, 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 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 6YRT · PDBe 6YRT · UniProt Q9HKI3
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