MolNFT v1 · #51778 · protein
Crystal structure of a pyrimidine degrading enzyme from drosophila melanogaster
2VHH · CG3027-pa: “Crystal structure of a pyrimidine degrading enzyme from drosophila melanogaster”. X-ray diffraction, 13 pockets (best druggability 0.79). MolNFT v1 #51778 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VHH
- Type
- protein
- Length
- 1,485 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG3027-pa
- EC
- 3.5.1.6
- UniProt
- Q9VI04
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CG3027-pa (EC 3.5.1.6) | protein | 345 | 31% helix, 24% strand | Q9VI04 |
| B, D | CG3027-pa (EC 3.5.1.6) | protein | 379 | 30% helix, 26% strand | Q9VI04 |
| C | CG3027-pa (EC 3.5.1.6) | protein | 382 | 30% helix, 26% strand | Q9VI04 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.79 | 0.92 | 44 | empty |
| 2 | 251 | 0.78 | 0.91 | 45 | empty |
| 3 | 823 | 0.75 | 0.80 | 83 | empty |
| 4 | 454 | 0.69 | 0.80 | 55 | empty |
| 5 | 488 | 0.69 | 0.79 | 59 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4170 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 4043 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 1275 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 763 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 761 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2VHH · 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 2VHH · PDBe 2VHH · UniProt Q9VI04
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