Research workbench
Crystal structure of the suca domain of mycobacterium smegmatis kgd (alpha-ketoglutarate decarboxylase), mutant R802A, in complex with gara
Analyse Crystal structure of the suca domain of mycobacterium smegmatis kgd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I2R
- Type
- protein
- Length
- 1,832 residues
- Chains
- 4
- 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
- TPP, MG, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% 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 | 824 | 45% helix, 15% strand | A0R2B1 |
| B | Glycogen accumulation regulator gara | protein | 94 | 0% helix, 52% strand | A0QYG2 |
| C | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 822 | 45% helix, 15% strand | A0R2B1 |
| D | Glycogen accumulation regulator gara | protein | 92 | 0% helix, 48% strand | A0QYG2 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.83 | 0.87 | 86 | TPP, MG |
| 2 | 737 | 0.81 | 0.85 | 94 | TPP, MG |
| 3 | 1075 | 0.75 | 0.78 | 118 | empty |
| 4 | 619 | 0.73 | 0.80 | 57 | empty |
| 5 | 425 | 0.65 | 0.78 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4807 Ų buried · 83 hydrogen bonds · protein-protein
- A–B · 1010 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 988 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6I2R · Crystal structure of the SucA domain of Mycobacterium smegmatis KGD (alpha-ketoglutarate… · 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 D against A, TM-score 0.97
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 6I2R · PDBe 6I2R · UniProt A0R2B1 · UniProt A0QYG2
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