MolNFT v1 · #106531 · protein
Structure of the gcpe-hmbpp complex from thermus thermophilius
4S23 · 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase: “Structure of the gcpe-hmbpp complex from thermus thermophilius”. X-ray diffraction, 2 ligands (SF4, H6P), 9 pockets (best druggability 0.81). MolNFT v1 #106531 on GenesisL1: 3D…
- PDB
- 4S23
- Type
- protein
- Length
- 810 residues
- Chains
- 2
- 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
- Q84GJ3
- Ligands
- SF4, H6P
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1) | protein | 405 | 47% helix, 17% strand | Q84GJ3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- H6P · (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.81 | 0.99 | 29 | SF4, H6P |
| 2 | 140 | 0.81 | 0.99 | 30 | H6P, SF4 |
| 3 | 807 | 0.73 | 0.78 | 77 | MES |
| 4 | 186 | 0.56 | 0.80 | 29 | empty |
| 5 | 188 | 0.48 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3267 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4S23 · Structure of the GcpE-HMBPP complex from Thermus thermophilius · the same entry in another collection · chain A against A, TM-score 1.00
- Q84GJ3 · AlphaFold monomer V2.0 prediction for 4-hydroxy-3-methylbut-2-en-1-yl diphosphate… · 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 Q84GJ3
- Elsewhere: RCSB PDB 4S23 · PDBe 4S23 · UniProt Q84GJ3
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