Research workbench
Crystal structure of a pyrimidine degrading enzyme from drosophila melanogaster
Analyse Crystal structure of a pyrimidine degrading enzyme from drosophila melanogaster in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VHI
- Type
- protein
- Length
- 2,969 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG3027-pa
- EC
- 3.5.1.6
- UniProt
- Q9VI04
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CG3027-pa (EC 3.5.1.6) | protein | 348 | 31% helix, 24% strand | Q9VI04 |
| B, D, F | CG3027-pa (EC 3.5.1.6) | protein | 379 | 31% helix, 25% strand | Q9VI04 |
| C, G | CG3027-pa (EC 3.5.1.6) | protein | 381 | 31% helix, 25% strand | Q9VI04 |
| E | CG3027-pa (EC 3.5.1.6) | protein | 380 | 31% helix, 25% strand | Q9VI04 |
| H | CG3027-pa (EC 3.5.1.6) | protein | 342 | 32% helix, 24% strand | Q9VI04 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.82 | 0.92 | 47 | empty |
| 2 | 280 | 0.81 | 0.93 | 45 | empty |
| 3 | 259 | 0.79 | 0.91 | 50 | empty |
| 4 | 328 | 0.78 | 0.89 | 51 | empty |
| 5 | 668 | 0.76 | 0.81 | 60 | empty |
Interfaces
13 interfaces between chains.
- C–D · 4079 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 4078 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 4071 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 4046 Ų buried · 55 hydrogen bonds · protein-protein
- D–E · 1284 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2VHI · Crystal structure of a pyrimidine degrading enzyme from Drosophila melanogaster · 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 Q9VI04
- Elsewhere: RCSB PDB 2VHI · PDBe 2VHI · UniProt Q9VI04
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