MolNFT v1 · #82419 · protein
3-isopropylmalate dehydrogenase from shewanella benthica DB21 mt-2
3VMK: “3-isopropylmalate dehydrogenase from shewanella benthica DB21 mt-2”. X-ray diffraction, 3 ligands (IPM, MG, CL), 6 pockets (best druggability 0.75). MolNFT v1 #82419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VMK
- Type
- protein
- Length
- 737 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- D2YZL2
- Ligands
- IPM, MG, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 369 | 47% helix, 20% strand | D2YZL2 |
| B | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 368 | 47% helix, 20% strand | D2YZL2 |
Ligands and binding sites
- IPM · 3-isopropylmalic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.75 | 0.79 | 78 | IPM, MG |
| 2 | 776 | 0.74 | 0.79 | 75 | IPM, MG |
| 3 | 207 | 0.58 | 0.80 | 23 | empty |
| 4 | 204 | 0.56 | 0.79 | 20 | empty |
| 5 | 68 | 0.31 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2552 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 3VMK · 3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2 · the same entry in another collection · chain A 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 D2YZL2
- Elsewhere: RCSB PDB 3VMK · PDBe 3VMK · UniProt D2YZL2
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