Research workbench
Crystal structure of staphylococcus epidermidis S192A mevalonate diphosphate decarboxylase complexed with inhibitor dpgp
Analyse Crystal structure of staphylococcus epidermidis S192A mevalonate diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DPY
- Type
- protein
- Length
- 651 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
- 2P0
- Pockets
- 5 · 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 | 40% helix, 26% strand | Q9FD73 |
| B | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 321 | 41% helix, 26% strand | Q9FD73 |
Ligands and binding sites
- 2P0 · 1-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}acetyl)-L-proline · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.84 | 0.87 | 90 | 2P0 |
| 2 | 317 | 0.74 | 0.86 | 43 | 2P0 |
| 3 | 63 | 0.55 | 0.87 | 16 | empty |
| 4 | 80 | 0.46 | 0.82 | 20 | empty |
| 5 | 71 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4DPY · Crystal structure of Staphylococcus epidermidis S192A mevalonate diphosphate… · 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 4DPY · PDBe 4DPY · UniProt Q9FD73
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