MolNFT v1 · #51991 · protein
Monoclinic form of idi-1
2VNQ · Isopentenyl-diphosphate delta-isomerase: “Monoclinic form of idi-1”. X-ray diffraction, 2 ligands (MN, SO4), 3 pockets (best druggability 0.70). MolNFT v1 #51991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VNQ
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl-diphosphate delta-isomerase
- EC
- 5.3.3.2
- UniProt
- Q46822
- Ligands
- MN, SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 176 | 27% helix, 34% strand | Q46822 |
| B | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 180 | 26% helix, 33% strand | Q46822 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.70 | 0.92 | 24 | IMD, SO4 |
| 2 | 133 | 0.64 | 0.87 | 33 | IMD, SO4 |
| 3 | 122 | 0.46 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 852 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 Q46822
- Elsewhere: RCSB PDB 2VNQ · PDBe 2VNQ · UniProt Q46822
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