MolNFT v1 · #60865 · protein
Crystal structure of human mevalonate diphosphate decarboxylase
3D4J · Diphosphomevalonate decarboxylase: “Crystal structure of human mevalonate diphosphate decarboxylase”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.74). MolNFT v1 #60865 on GenesisL1: 3D structure, binding sites…
- PDB
- 3D4J
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphosphomevalonate decarboxylase
- EC
- 4.1.1.33
- UniProt
- P53602
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 374 | 37% helix, 22% strand | P53602 |
| B | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 368 | 37% helix, 23% strand | P53602 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.74 | 0.82 | 67 | SO4 |
| 2 | 293 | 0.74 | 0.86 | 44 | SO4 |
| 3 | 559 | 0.69 | 0.78 | 70 | empty |
| 4 | 151 | 0.51 | 0.79 | 20 | empty |
| 5 | 50 | 0.24 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1169 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3D4J · Crystal structure of Human mevalonate diphosphate decarboxylase · the same entry in another collection · chain A against A, TM-score 1.00
- P53602 · AlphaFold monomer V2.0 prediction for diphosphomevalonate decarboxylase (P53602) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P53602
- Elsewhere: RCSB PDB 3D4J · PDBe 3D4J · UniProt P53602
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