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The crystal structure of fbia from mycobacterium smegmatis, dehydro- F420-0 bound form
Analyse The crystal structure of fbia from mycobacterium smegmatis, dehydro- F420-0… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UW7
- Type
- protein
- Length
- 632 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
- QMD, CA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Phosphoenolpyruvate transferase (EC 2.7.8.28) | protein | 318 | 40% helix, 19% strand | A0QTG2 |
| A | Phosphoenolpyruvate transferase (EC 2.7.8.28) | protein | 314 | 40% helix, 20% strand | A0QTG2 |
Ligands and binding sites
- QMD · 2-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[2,4,8-tris(oxidanylidene)-1,9-dihydropyrimido[4,5-b]quinolin-10-yl]pentoxy]phosphoryl]oxyprop-2-enoic acid · ligand · chains B
- CA · Calcium ion · metal · 2 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.65 | 0.80 | 44 | QMD |
| 2 | 475 | 0.60 | 0.74 | 55 | empty |
| 3 | 55 | 0.40 | 0.81 | 15 | GOL |
| 4 | 73 | 0.31 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 1208 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6UW7 · The crystal structure of FbiA from Mycobacterium smegmatis, Dehydro-F420-0 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 6UW7 · PDBe 6UW7 · UniProt A0QTG2
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