Research workbench
Crystal structure of D. melanogaster pur-alpha repeat III.
Analyse Crystal structure of D. melanogaster pur-alpha repeat III. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FGO
- Type
- protein
- Length
- 381 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG1507-pb, isoform B
- UniProt
- Q9V4D9
- Ligands
- CL
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CG1507-pb, isoform B | protein | 62 | 26% helix, 50% strand | Q9V4D9 |
| B | CG1507-pb, isoform B | protein | 65 | 25% helix, 51% strand | Q9V4D9 |
| C | CG1507-pb, isoform B | protein | 61 | 28% helix, 49% strand | Q9V4D9 |
| D | CG1507-pb, isoform B | protein | 66 | 21% helix, 52% strand | Q9V4D9 |
| E | CG1507-pb, isoform B | protein | 64 | 27% helix, 48% strand | Q9V4D9 |
| F | CG1507-pb, isoform B | protein | 63 | 29% helix, 49% strand | Q9V4D9 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.82 | 0.84 | 93 | empty |
| 2 | 393 | 0.76 | 0.86 | 60 | empty |
| 3 | 78 | 0.38 | 0.78 | 15 | empty |
| 4 | 59 | 0.26 | 0.73 | 13 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2045 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1994 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1949 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 639 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 458 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5FGO · Crystal structure of D. melanogaster Pur-alpha repeat III. · 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 Q9V4D9
- Elsewhere: RCSB PDB 5FGO · PDBe 5FGO · UniProt Q9V4D9
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