Research workbench
Crystal structure of the H747A mutant of the suca domain of mycobacterium smegmatis kgd showing the active site lid closed
Analyse Crystal structure of the H747A mutant of the suca domain of mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZHR
- Type
- protein
- Length
- 3,281 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
- TPP, MG, CA
- Pockets
- 20 · best druggability 0.91
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 | 822 | 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 | 823 | 45% 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 | 813 | 45% 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 | 823 | 44% helix, 15% strand | A0R2B1 |
Ligands and binding sites
- TPP · Thiamine diphosphate · 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
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.91 | 0.94 | 104 | TPP, MG |
| 2 | 454 | 0.87 | 0.95 | 67 | TPP, MG |
| 3 | 422 | 0.86 | 0.94 | 52 | TPP, MG |
| 4 | 859 | 0.78 | 0.81 | 89 | empty |
| 5 | 804 | 0.73 | 0.78 | 90 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5096 Ų buried · 114 hydrogen bonds · protein-protein
- C–D · 5025 Ų buried · 112 hydrogen bonds · protein-protein
- A–C · 652 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3ZHR · Crystal structure of the H747A mutant of the SucA domain of Mycobacterium smegmatis KGD… · 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 C 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
- Elsewhere: RCSB PDB 3ZHR · PDBe 3ZHR · UniProt A0R2B1
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