Research workbench
Crystal structure of staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-fmvapp
Analyse Crystal structure of staphylococcus epidermidis mevalonate diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QT7
- Type
- protein
- Length
- 644 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
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 324 | 41% helix, 26% strand | Q9FD73 |
| B | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 320 | 42% helix, 27% 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
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 | 361 | 0.73 | 0.84 | 50 | FM0 |
| 2 | 259 | 0.69 | 0.84 | 45 | FM0 |
| 3 | 121 | 0.56 | 0.83 | 16 | empty |
| 4 | 87 | 0.33 | 0.74 | 25 | empty |
| 5 | 64 | 0.32 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1001 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3QT7 · Crystal structure of 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 3QT7 · PDBe 3QT7 · UniProt Q9FD73
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