MolNFT v1 · #171062 · protein
Transaldolase variant D211A from T. acidophilum in complex with D- fructose 6-phosphate schiff-base intermediate
6YS0 · Probable transaldolase: “Transaldolase variant D211A from T. acidophilum in complex with D- fructose 6-phosphate schiff-base…”. X-ray diffraction, 1 ligand (F6R), 11 pockets (best druggability 0.51). MolNFT v1 #171062 on GenesisL1…
- PDB
- 6YS0
- Type
- protein
- Length
- 1,096 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
- 11 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 52% 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 | 50% helix, 17% strand | Q9HKI3 |
| E | Probable transaldolase (EC 2.2.1.2) | protein | 216 | 52% 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, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.51 | 0.81 | 19 | empty |
| 2 | 84 | 0.48 | 0.82 | 18 | empty |
| 3 | 111 | 0.47 | 0.79 | 17 | empty |
| 4 | 115 | 0.46 | 0.78 | 29 | F6R |
| 5 | 121 | 0.44 | 0.77 | 21 | F6R |
Interfaces
5 interfaces between chains.
- B–C · 1821 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1816 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1539 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1479 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1429 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6YS0 · Transaldolase variant D211A from T. acidophilum in complex with D-fructose 6-phosphate… · the same entry in another collection · chain E against E, 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 6YS0 · PDBe 6YS0 · UniProt Q9HKI3
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