Research workbench
Structure of the gcpe-mecpp (ispg) complex from thermus thermophilus
Analyse Structure of the gcpe-mecpp (ispg) complex from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G9P
- Type
- protein
- Length
- 405 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
- Q72H18
- Ligands
- SF4, CDI, K, CL
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 48% 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 | 405 | 48% helix, 17% strand | Q72H18 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- CDI · 2C-methyl-D-erythritol 2,4-cyclodiphosphate · ligand · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · 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 | 108 | 0.45 | 0.79 | 14 | MES |
| 2 | 187 | 0.44 | 0.73 | 21 | MES |
| 3 | 82 | 0.35 | 0.76 | 20 | CDI |
Compared structures
- 4G9P · Structure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q72H18 · 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 1.00
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 Q72H18
- Elsewhere: RCSB PDB 4G9P · PDBe 4G9P · UniProt Q72H18
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