Research workbench
The crystal structure of fbia from mycobacterium smegmatis, GDP and fo bound form
Analyse The crystal structure of fbia from mycobacterium smegmatis, GDP and fo bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UW5
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate transferase
- EC
- 2.7.8.28
- UniProt
- A0QTG2
- Ligands
- GDP, FO1, CA
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Phosphoenolpyruvate transferase (EC 2.7.8.28) | protein | 326 | 39% helix, 19% strand | A0QTG2 |
| A | Phosphoenolpyruvate transferase (EC 2.7.8.28) | protein | 320 | 40% helix, 20% strand | A0QTG2 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, A
- FO1 · 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol · ligand · chains B
- CA · Calcium ion · metal · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.77 | 0.85 | 53 | GDP, FO1, CA |
| 2 | 641 | 0.65 | 0.75 | 66 | GDP |
Interfaces
1 interface between chains.
- B–A · 1235 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6UW5 · The crystal structure of FbiA from Mycobacterium smegmatis, GDP and Fo bound form · the same entry in another collection · chain B against B, TM-score 1.00
- A0QTG2 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate transferase (A0QTG2) · a predicted model of the same protein · chain B 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 A0QTG2
- Elsewhere: RCSB PDB 6UW5 · PDBe 6UW5 · UniProt A0QTG2
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