MolNFT v1 · #76711 · protein
Crystal structure of staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor dpgp
3QT6: “Crystal structure of staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor…”. X-ray diffraction, 1 ligand (2P0), 3 pockets (best druggability 0.74). MolNFT v1 #76711 on GenesisL1: 3D structure…
- PDB
- 3QT6
- Type
- protein
- Length
- 649 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
- 3 · best druggability 0.74
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 | 328 | 41% helix, 26% strand | Q9FD73 |
| B | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 321 | 42% 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
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 | 786 | 0.74 | 0.79 | 85 | 2P0 |
| 2 | 415 | 0.71 | 0.82 | 49 | 2P0 |
| 3 | 53 | 0.29 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1026 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3QT6 · 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 3QT6 · PDBe 3QT6 · UniProt Q9FD73
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