MolNFT v1 · #151947 · protein
Crystal structure of the suca domain of mycobacterium smegmatis kgd (R802A) in complex with gara, following 2-oxoglutarate soak
6I2S · Multifunctional 2-oxoglutarate metabolism enzyme: “Crystal structure of the suca domain of mycobacterium smegmatis kgd (R802A) in complex with gara, following…”. X-ray diffraction, 4 ligands (TD6, MG, CA), 12 pockets (best…
- PDB
- 6I2S
- Type
- protein
- Length
- 927 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multifunctional 2-oxoglutarate metabolism enzyme; Glycogen accumulation regulator gara
- EC
- 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61
- UniProt
- A0R2B1, A0QYG2
- Ligands
- TD6, MG, CA, PO4
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 830 | 44% helix, 16% strand | A0R2B1 |
| B | Glycogen accumulation regulator gara | protein | 97 | 0% helix, 51% strand | A0QYG2 |
Ligands and binding sites
- TD6 · (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.62 | 0.84 | 24 | empty |
| 2 | 197 | 0.61 | 0.82 | 31 | MG, TD6 |
| 3 | 371 | 0.61 | 0.77 | 42 | empty |
| 4 | 253 | 0.56 | 0.77 | 28 | empty |
| 5 | 188 | 0.50 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1002 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6I2S · Crystal structure of the SucA domain of Mycobacterium smegmatis KGD (R802A) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- A0QYG2 · AlphaFold monomer V2.0 prediction for glycogen accumulation regulator gara (A0QYG2) · a predicted model of the same protein · chain B against A, TM-score 0.98
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
- Every structure of UniProt A0QYG2
- Elsewhere: RCSB PDB 6I2S · PDBe 6I2S · UniProt A0R2B1 · UniProt A0QYG2
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