MolNFT v1 · #84342 · protein
Crystal structure of the suca domain of mycobacterium smegmatis kgd, second post-decarboxylation intermediate from 2-oxoadipate
3ZHU · Multifunctional 2-oxoglutarate metabolism enzyme: “Crystal structure of the suca domain of mycobacterium smegmatis kgd, second post-decarboxylation intermediate…”. X-ray diffraction, 3 ligands (TD8, MG, CA), 20 pockets (best…
- PDB
- 3ZHU
- Type
- protein
- Length
- 3,380 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
- TD8, MG, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 43% 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 | 847 | 43% 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 | 836 | 43% 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 | 845 | 44% helix, 14% 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 | 852 | 43% helix, 15% strand | A0R2B1 |
Ligands and binding sites
- TD8 · (5R)-5-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-5-(2-{[(phosphonatooxy)phosphinato]oxy}ethyl)-1,3-thiazol-3-ium-2-yl}-5-hydroxypentanoate · 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 | 986 | 0.88 | 0.89 | 169 | TD8 |
| 2 | 768 | 0.86 | 0.90 | 141 | TD8 |
| 3 | 1071 | 0.79 | 0.81 | 116 | empty |
| 4 | 818 | 0.77 | 0.81 | 88 | empty |
| 5 | 724 | 0.73 | 0.79 | 64 | empty |
Interfaces
3 interfaces between chains.
- C–D · 5639 Ų buried · 108 hydrogen bonds · protein-protein
- A–B · 5545 Ų buried · 105 hydrogen bonds · protein-protein
- A–D · 335 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3ZHU · Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, second… · 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 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 3ZHU · PDBe 3ZHU · UniProt A0R2B1
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