Research workbench
Crystal structures of escherichia COLI isph in complex with tmbpp a potent inhibitor of the methylerythritol phosphate pathway
Analyse Crystal structures of escherichia COLI isph in complex with tmbpp a potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZGN
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
- EC
- 1.17.1.2
- UniProt
- P62623
- Ligands
- 10G, SF4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 309 | 42% helix, 17% strand | P62623 |
Ligands and binding sites
- 10G · (2E)-3-methyl-4-sulfanylbut-2-en-1-yl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.80 | 0.98 | 28 | SF4, 10G |
| 2 | 140 | 0.80 | 0.97 | 27 | 10G, SF4 |
| 3 | 863 | 0.72 | 0.77 | 85 | empty |
| 4 | 101 | 0.39 | 0.76 | 19 | empty |
| 5 | 74 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 390 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ZGN · Crystal structures of Escherichia coli IspH in complex with TMBPP a potent inhibitor of… · the same entry in another collection · chain A against A, TM-score 1.00
- P62623 · AlphaFold monomer V2.0 prediction for 4-hydroxy-3-methylbut-2-enyl diphosphate reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P62623
- Elsewhere: RCSB PDB 3ZGN · PDBe 3ZGN · UniProt P62623
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