MolNFT v1 · #157483 · protein
Crystal structure of anaerolinea thermophila mevalonate 5-phosphate decarboxylase complexed with (R)-mvap
6N0X · Diphosphomevalonate decarboxylase: “Crystal structure of anaerolinea thermophila mevalonate 5-phosphate decarboxylase complexed with (R)-mvap”. X-ray diffraction, 1 ligand (PMV), 20 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 6N0X
- Type
- protein
- Length
- 1,925 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphosphomevalonate decarboxylase
- EC
- 4.1.1.33
- UniProt
- E8N6F3
- Ligands
- PMV
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 321 | 40% helix, 26% strand | E8N6F3 |
| B | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 320 | 41% helix, 27% strand | E8N6F3 |
| C | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 324 | 41% helix, 26% strand | E8N6F3 |
| D | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 323 | 41% helix, 26% strand | E8N6F3 |
| E | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 320 | 40% helix, 26% strand | E8N6F3 |
| F | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 317 | 41% helix, 25% strand | E8N6F3 |
Ligands and binding sites
- PMV · (3R)-3-hydroxy-3-methyl-5-(phosphonooxy)pentanoic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.74 | 0.84 | 53 | PMV |
| 2 | 338 | 0.73 | 0.85 | 51 | PMV |
| 3 | 520 | 0.73 | 0.81 | 69 | PMV |
| 4 | 203 | 0.71 | 0.88 | 55 | empty |
| 5 | 320 | 0.71 | 0.84 | 45 | PMV |
Interfaces
5 interfaces between chains.
- A–E · 1134 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1130 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 1128 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1001 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 741 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6N0X · Crystal structure of Anaerolinea thermophila mevalonate 5-phosphate decarboxylase… · 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 E8N6F3
- Elsewhere: RCSB PDB 6N0X · PDBe 6N0X · UniProt E8N6F3
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