MolNFT v1 · #147109 · protein
Mddef in complex with mvapp
6E2T · Mevalonate diphosphate decarboxylase: “Mddef in complex with mvapp”. X-ray diffraction, 1 ligand (DP6), 2 pockets (best druggability 0.69). MolNFT v1 #147109 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6E2T
- Type
- protein
- Length
- 320 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mevalonate diphosphate decarboxylase
- EC
- 4.1.1.33
- UniProt
- Q9FD68
- Ligands
- DP6
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 320 | 42% helix, 27% strand | Q9FD68 |
Ligands and binding sites
- DP6 · (3R)-3-hydroxy-5-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylpentanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.69 | 0.79 | 56 | DP6 |
| 2 | 77 | 0.35 | 0.76 | 17 | empty |
Compared structures
- 6E2T · MDDEF in complex with MVAPP · 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 Q9FD68
- Elsewhere: RCSB PDB 6E2T · PDBe 6E2T · UniProt Q9FD68
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