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Ambient temperature structure of bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate
Analyse Ambient temperature structure of bifidobacgterium longum phosphoketolase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C8I
- Type
- protein
- Length
- 6,465 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylulose-5-PHOSPHATE/FRUCTOSE-6-phosphate phosphoketolase
- EC
- 4.1.2.22
- UniProt
- Q6R2Q7
- Ligands
- PEP, TPP, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Xylulose-5-PHOSPHATE/FRUCTOSE-6-phosphate phosphoketolase (EC 4.1.2.22) | protein | 808 | 43% helix, 14% strand | Q6R2Q7 |
| B | Xylulose-5-PHOSPHATE/FRUCTOSE-6-phosphate phosphoketolase (EC 4.1.2.22) | protein | 811 | 43% helix, 14% strand | Q6R2Q7 |
| C | Xylulose-5-PHOSPHATE/FRUCTOSE-6-phosphate phosphoketolase (EC 4.1.2.22) | protein | 806 | 42% helix, 15% strand | Q6R2Q7 |
| D, G | Xylulose-5-PHOSPHATE/FRUCTOSE-6-phosphate phosphoketolase (EC 4.1.2.22) | protein | 807 | 41% helix, 15% strand | Q6R2Q7 |
| E, F | Xylulose-5-PHOSPHATE/FRUCTOSE-6-phosphate phosphoketolase (EC 4.1.2.22) | protein | 809 | 43% helix, 15% strand | Q6R2Q7 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- TPP · Thiamine diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.79 | 0.81 | 111 | PEP, TPP, CA |
| 2 | 739 | 0.78 | 0.82 | 97 | PEP, TPP, CA |
| 3 | 827 | 0.76 | 0.80 | 97 | TPP, CA, PEP |
| 4 | 69 | 0.75 | 0.99 | 17 | empty |
| 5 | 75 | 0.75 | 0.98 | 15 | empty |
Interfaces
16 interfaces between chains.
- C–D · 5431 Ų buried · 110 hydrogen bonds · protein-protein
- E–F · 5404 Ų buried · 109 hydrogen bonds · protein-protein
- G–H · 5343 Ų buried · 110 hydrogen bonds · protein-protein
- A–B · 5276 Ų buried · 107 hydrogen bonds · protein-protein
- D–E · 553 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7C8I · Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine… · the same entry in another collection · 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 Q6R2Q7
- Elsewhere: RCSB PDB 7C8I · PDBe 7C8I · UniProt Q6R2Q7
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