Research workbench
Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes
Analyse Structure of butyrate kinase 2 reveals both open- and citrate-induced closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X9J
- Type
- protein
- Length
- 2,976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable butyrate kinase 2
- EC
- 2.7.2.7
- UniProt
- Q9X278
- Ligands
- NA, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Probable butyrate kinase 2 (EC 2.7.2.7) | protein | 373 | 43% helix, 20% strand | Q9X278 |
| B, C, E | Probable butyrate kinase 2 (EC 2.7.2.7) | protein | 371 | 43% helix, 20% strand | Q9X278 |
| F, H | Probable butyrate kinase 2 (EC 2.7.2.7) | protein | 372 | 43% helix, 19% strand | Q9X278 |
Ligands and binding sites
- NA · Sodium ion · metal · chains D
- PO4 · Phosphate ion · ion · 5 copies · chains B, C, D, E, F, G, A, H
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, F
- CIT · Citric acid · additive · 4 copies · chains D, C, 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 | 825 | 0.85 | 0.88 | 97 | GOL |
| 2 | 754 | 0.84 | 0.88 | 92 | CIT |
| 3 | 778 | 0.84 | 0.87 | 77 | CIT |
| 4 | 149 | 0.80 | 0.97 | 36 | PO4 |
| 5 | 124 | 0.78 | 0.97 | 37 | PO4 |
Interfaces
8 interfaces between chains.
- A–H · 3541 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 3530 Ų buried · 33 hydrogen bonds · protein-protein
- F–G · 3503 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 3432 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1225 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1X9J · Structure of butyrate kinase 2 reveals both open- and citrate-induced closed… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9X278 · AlphaFold monomer V2.0 prediction for probable butyrate kinase 2 (Q9X278) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9X278
- Elsewhere: RCSB PDB 1X9J · PDBe 1X9J · UniProt Q9X278
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