MolNFT v1 · #72995 · protein
Crystal structure of ispg (gcpe)
3NOY · 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase: “Crystal structure of ispg (gcpe)”. X-ray diffraction, 1 ligand (SF4), 8 pockets (best druggability 0.78). MolNFT v1 #72995 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3NOY
- Type
- protein
- Length
- 1,401 residues
- Chains
- 4
- 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
- O67496
- Ligands
- SF4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% 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 | 349 | 44% helix, 20% strand | O67496 |
| B, C | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) | protein | 351 | 42% helix, 20% strand | O67496 |
| D | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) | protein | 350 | 42% helix, 19% strand | O67496 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.78 | 0.80 | 70 | empty |
| 2 | 712 | 0.75 | 0.81 | 83 | empty |
| 3 | 583 | 0.73 | 0.80 | 57 | empty |
| 4 | 718 | 0.72 | 0.79 | 77 | empty |
| 5 | 689 | 0.72 | 0.79 | 71 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1941 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1933 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 577 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 O67496
- Elsewhere: RCSB PDB 3NOY · PDBe 3NOY · UniProt O67496
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