MolNFT v1 · #106576 · protein
Ispg in complex with epoxide intermediate
4S3C · 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase: “Ispg in complex with epoxide intermediate”. X-ray diffraction, 2 ligands (43Q, SF4), 3 pockets (best druggability 0.44). MolNFT v1 #106576 on GenesisL1: 3D structure, binding…
- PDB
- 4S3C
- Type
- protein
- Length
- 402 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
- EC
- 1.17.7.1
- UniProt
- Q5SLI8
- Ligands
- 43Q, SF4
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) | protein | 402 | 49% helix, 17% strand | Q5SLI8 |
Ligands and binding sites
- 43Q · (3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium, carbokation intermediate · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.44 | 0.75 | 25 | GOL |
| 2 | 116 | 0.42 | 0.76 | 16 | empty |
| 3 | 102 | 0.37 | 0.76 | 22 | empty |
Modifications
Observed in the structure: 1 modified (carboxylation).
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 Q5SLI8
- Elsewhere: RCSB PDB 4S3C · PDBe 4S3C · UniProt Q5SLI8
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