MolNFT v1 · #89462 · protein
Crystal structure of S192A staphylococcus epidermidis mevalonate diphosphate decarboxylase
4DPX: “Crystal structure of S192A staphylococcus epidermidis mevalonate diphosphate decarboxylase”. X-ray diffraction, 4 pockets (best druggability 0.84). MolNFT v1 #89462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DPX
- Type
- protein
- Length
- 652 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
- Pockets
- 4 · 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, 26% strand | Q9FD73 |
| B | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 322 | 40% helix, 26% strand | Q9FD73 |
Ligands and binding sites
- FMT · Formic acid · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.84 | 0.86 | 88 | GOL, FMT |
| 2 | 304 | 0.73 | 0.86 | 44 | GOL, FMT |
| 3 | 78 | 0.57 | 0.87 | 15 | empty |
| 4 | 64 | 0.43 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1267 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4DPX · Crystal structure of S192A Staphylococcus epidermidis mevalonate diphosphate decarboxylase · the same entry in another collection · chain B against B, 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 4DPX · PDBe 4DPX · UniProt Q9FD73
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