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Crystal structure of the suca domain of mycobacterium smegmatis kgd, first post-decarboxylation intermediate from alpha-ketoglutarate
Analyse Crystal structure of the suca domain of mycobacterium smegmatis kgd, first… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZHS
- Type
- protein
- Length
- 3,248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multifunctional 2-oxoglutarate metabolism enzyme
- EC
- 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61
- UniProt
- A0R2B1
- Ligands
- TD6, MG, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 15% 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 | 817 | 45% helix, 15% strand | A0R2B1 |
| B | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 813 | 44% helix, 15% strand | A0R2B1 |
| C | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 808 | 44% helix, 15% strand | A0R2B1 |
| D | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 810 | 45% helix, 15% strand | A0R2B1 |
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 · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.82 | 0.86 | 105 | TD6 |
| 2 | 610 | 0.81 | 0.86 | 96 | TD6, MG |
| 3 | 571 | 0.80 | 0.86 | 88 | TD6, MG |
| 4 | 1090 | 0.80 | 0.82 | 101 | empty |
| 5 | 600 | 0.79 | 0.85 | 87 | TD6 |
Interfaces
3 interfaces between chains.
- A–B · 4627 Ų buried · 93 hydrogen bonds · protein-protein
- C–D · 4548 Ų buried · 87 hydrogen bonds · protein-protein
- A–C · 823 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3ZHS · Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, first… · the same entry in another collection · chain D against D, 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 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 A0R2B1
- Elsewhere: RCSB PDB 3ZHS · PDBe 3ZHS · UniProt A0R2B1
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