MolNFT v1 · #120009 · protein
Crystal structure of sulfolobus solfataricus diphosphomevalonate decarboxylase in complex with ATP-gamma-S
5GMD: “Crystal structure of sulfolobus solfataricus diphosphomevalonate decarboxylase in complex with ATP-gamma-S”. X-ray diffraction, 4 ligands (DP6, AGS, AMP), 1 pocket (best druggability 0.78). MolNFT v1 #120009 on GenesisL1: 3D…
- PDB
- 5GMD
- Type
- protein
- Length
- 325 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphosphomevalonate decarboxylase
- EC
- 4.1.1.33
- UniProt
- Q97UL5
- Ligands
- DP6, AGS, AMP, SO4
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 325 | 42% helix, 23% strand | Q97UL5 |
Ligands and binding sites
- DP6 · (3R)-3-hydroxy-5-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylpentanoic acid · ligand · chains A
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.78 | 0.83 | 70 | DP6, AGS, SO4 |
Compared structures
- 5GMD · Crystal structure of Sulfolobus solfataricus diphosphomevalonate decarboxylase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97UL5 · AlphaFold monomer V2.0 prediction for diphosphomevalonate decarboxylase (Q97UL5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q97UL5
- Elsewhere: RCSB PDB 5GMD · PDBe 5GMD · UniProt Q97UL5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.