MolNFT v1 · #89459 · protein
Crystal structure of staphylococcus epidermidis S192A mevalonate diphosphate decarboxylase complexed with inhibitor 6-fmvapp and atpgs
4DPU: “Crystal structure of staphylococcus epidermidis S192A mevalonate diphosphate decarboxylase complexed with…”. X-ray diffraction, 2 ligands (FM0, AGS), 3 pockets (best druggability 0.84). MolNFT v1 #89459 on GenesisL1: 3D structure…
- PDB
- 4DPU
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mevalonate diphosphate decarboxylase
- EC
- 4.1.1.33
- UniProt
- Q9FD73
- Ligands
- FM0, AGS
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 330 | 42% helix, 25% strand | Q9FD73 |
| B | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 326 | 41% helix, 26% strand | Q9FD73 |
Ligands and binding sites
- FM0 · (3R)-3-(fluoromethyl)-3-hydroxy-5-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}pentanoic acid · ligand · 2 copies · chains A, B
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.84 | 0.85 | 85 | FM0, AGS |
| 2 | 685 | 0.80 | 0.84 | 79 | FM0, AGS |
| 3 | 80 | 0.34 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 964 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4DPU · Crystal structure of Staphylococcus epidermidis S192A mevalonate diphosphate… · the same entry in another collection · 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 Q9FD73
- Elsewhere: RCSB PDB 4DPU · PDBe 4DPU · UniProt Q9FD73
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