MolNFT v1 · #169926 · protein
Crystal structure of diphosphomevalonate decarboxylase (MVD1) cryptococcus neoformans var. grubii serotype a
6XR5: “Crystal structure of diphosphomevalonate decarboxylase (MVD1) cryptococcus neoformans var. grubii serotype a”. X-ray diffraction, 2 ligands (ADE, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #169926 on GenesisL1: 3D…
- PDB
- 6XR5
- Type
- protein
- Length
- 3,120 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphosphomevalonate decarboxylase
- EC
- 4.1.1.33
- UniProt
- J9VRT5
- Ligands
- ADE, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 392 | 38% helix, 22% strand | J9VRT5 |
| B | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 391 | 38% helix, 23% strand | J9VRT5 |
| C | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 386 | 39% helix, 22% strand | J9VRT5 |
| D | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 393 | 38% helix, 22% strand | J9VRT5 |
| E | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 386 | 39% helix, 22% strand | J9VRT5 |
| F | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 387 | 38% helix, 22% strand | J9VRT5 |
| G | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | protein | 393 | 37% helix, 22% strand | J9VRT5 |
Ligands and binding sites
- ADE · Adenine · ligand · 5 copies · chains A, B, D, E, H
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F, H
- EDO · 1,2-ethanediol · additive · 2 copies · chains F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.79 | 0.81 | 112 | empty |
| 2 | 703 | 0.76 | 0.81 | 80 | empty |
| 3 | 485 | 0.75 | 0.83 | 67 | SO4, ADE |
| 4 | 466 | 0.74 | 0.83 | 59 | SO4, ADE |
| 5 | 63 | 0.74 | 0.99 | 20 | empty |
Interfaces
14 interfaces between chains.
- C–H · 1354 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 1311 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1307 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 1248 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 478 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6XR5 · Crystal Structure of Diphosphomevalonate decarboxylase (MVD1) Cryptococcus neoformans… · 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 J9VRT5
- Elsewhere: RCSB PDB 6XR5 · PDBe 6XR5 · UniProt J9VRT5
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