Research workbench
1.48 ångström resolution crystal structure of transaldolase from thermoplasma acidophilum in complex with D-fructose 6-phosphate schiff-base intermediate
Analyse 1.48 ångström resolution crystal structure of transaldolase from thermoplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YR3
- 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
- Ligands
- F6R
- Pockets
- 7 · best druggability 0.44
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
- F6R · Fructose -6-phosphate · ligand · 5 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 6 copies · chains A, E, B, C
- GOL · Glycerol · 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
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.44 | 0.78 | 26 | F6R |
| 2 | 109 | 0.42 | 0.77 | 28 | F6R |
| 3 | 104 | 0.42 | 0.77 | 26 | F6R |
| 4 | 108 | 0.41 | 0.77 | 25 | F6R |
| 5 | 92 | 0.39 | 0.77 | 24 | F6R |
Interfaces
5 interfaces between chains.
- B–C · 1829 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1829 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1810 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1757 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1751 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6YR3 · 1.48 Angstrom Resolution Crystal Structure of Transaldolase from Thermoplasma acidophilum… · 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 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 6YR3 · PDBe 6YR3 · UniProt Q9HKI3
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