Research workbench
Crystal structure of the suca domain of mycobacterium smegmatis alpha-ketoglutarate decarboxylase in complex with the enamine-thdp intermediate
Analyse Crystal structure of the suca domain of mycobacterium smegmatis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YID
- Type
- protein
- Length
- 3,376 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate decarboxylase
- EC
- 4.1.1.71
- UniProt
- A0R2B1
- Ligands
- TD7, MG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoglutarate decarboxylase (EC 4.1.1.71) | protein | 844 | 44% helix, 15% strand | A0R2B1 |
| B | 2-oxoglutarate decarboxylase (EC 4.1.1.71) | protein | 837 | 43% helix, 15% strand | A0R2B1 |
| C | 2-oxoglutarate decarboxylase (EC 4.1.1.71) | protein | 843 | 45% helix, 14% strand | A0R2B1 |
| D | 2-oxoglutarate decarboxylase (EC 4.1.1.71) | protein | 852 | 44% helix, 15% strand | A0R2B1 |
Ligands and binding sites
- TD7 · (4E)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-2(3H)-ylidene}-4-hydroxybutanoic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
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 | 715 | 0.86 | 0.90 | 130 | TD7 |
| 2 | 818 | 0.85 | 0.88 | 133 | TD7, MG |
| 3 | 866 | 0.78 | 0.81 | 92 | empty |
| 4 | 867 | 0.77 | 0.81 | 104 | empty |
| 5 | 692 | 0.73 | 0.79 | 66 | empty |
Interfaces
3 interfaces between chains.
- C–D · 5599 Ų buried · 107 hydrogen bonds · protein-protein
- A–B · 5529 Ų buried · 101 hydrogen bonds · protein-protein
- A–D · 282 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2YID · Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate… · the same entry in another collection · chain A against A, TM-score 1.00
- A0R2B1 · AlphaFold monomer V2.0 prediction for multifunctional 2-oxoglutarate metabolism enzyme… · a predicted model of the same protein · chain B 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 A0R2B1
- Elsewhere: RCSB PDB 2YID · PDBe 2YID · UniProt A0R2B1
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