MolNFT v2 · #24761 · protein
The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans
1V5B: “The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans”. X-ray diffraction at 2.95, 1 ligand (SO4), 20 pockets (best druggability 0.82). MolNFT v2 #24761 on GenesisL1: 3D structure…
- PDB
- 1V5B
- Type
- protein
- Length
- 2,853 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.95
- Source
- Bacillus coagulans
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- P12010
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.95 · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 356 | 42% helix, 22% strand | P12010 |
| B, D, F, G, H | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 357 | 43% helix, 21% strand | P12010 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.82 | 0.83 | 109 | SO4 |
| 2 | 158 | 0.64 | 0.85 | 32 | empty |
| 3 | 446 | 0.63 | 0.77 | 31 | empty |
| 4 | 459 | 0.61 | 0.76 | 48 | empty |
| 5 | 434 | 0.60 | 0.75 | 47 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2206 Ų buried · 47 hydrogen bonds · protein-protein
- G–H · 2160 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2141 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2102 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1V5B · The structure of the mutant, S225A and E251L, of 3-isopropylmalate dehydrogenase from… · the same entry in another collection · chain H against H, TM-score 1.00
- P12010 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (P12010) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P12010
- Elsewhere: RCSB PDB 1V5B · PDBe 1V5B · UniProt P12010
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