Research workbench
Mddef in complex with mvapp, ADP, sulfate and cobalt. anomalous data
Analyse Mddef in complex with mvapp, ADP, sulfate and cobalt. anomalous data in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E2Y
- Type
- protein
- Length
- 327 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
- ADP, DP6, CO, SO4
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mevalonate diphosphate decarboxylase (EC 4.1.1.33) | protein | 327 | 40% helix, 26% strand | Q9FD68 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- DP6 · (3R)-3-hydroxy-5-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylpentanoic acid · ligand · chains A
- CO · Cobalt (II) ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 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 | 488 | 0.79 | 0.86 | 50 | SO4, ADP, DP6, CO |
| 2 | 58 | 0.33 | 0.77 | 18 | empty |
Compared structures
- 6E2Y · MDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data · 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 6E2Y · PDBe 6E2Y · UniProt Q9FD68
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