Research workbench
X-ray structure of a putative thiamin diphosphate-dependent enzyme isolated from mycobacterium smegmatis
Analyse X-ray structure of a putative thiamin diphosphate-dependent enzyme isolated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q9D
- Type
- protein
- Length
- 1,036 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoylformate decarboxylase
- EC
- 4.1.1.7
- UniProt
- A0QSU7
- Ligands
- MG
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 517 | 38% helix, 19% strand | A0QSU7 |
| B | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 519 | 37% helix, 19% strand | A0QSU7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.84 | 0.85 | 116 | empty |
| 2 | 624 | 0.69 | 0.77 | 83 | MG, FMT |
| 3 | 354 | 0.65 | 0.80 | 58 | MG, FMT |
| 4 | 362 | 0.61 | 0.77 | 47 | empty |
| 5 | 81 | 0.40 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1293 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 4Q9D · X-ray structure of a putative thiamin diphosphate-dependent enzyme isolated from… · 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 A0QSU7
- Elsewhere: RCSB PDB 4Q9D · PDBe 4Q9D · UniProt A0QSU7
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