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Crystal structure of dava-4
Analyse Crystal structure of dava-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3USF
- Type
- protein
- Length
- 829 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate-1-semialdehyde 2,1-aminomutase
- EC
- 5.4.3.8
- UniProt
- Q31QJ2
- Ligands
- PLR, HOZ
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 427 | 42% helix, 17% strand | Q31QJ2 |
| B | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 402 | 42% helix, 17% strand | Q31QJ2 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- HOZ · (4S)-4,5-diaminopentanoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.82 | 0.97 | 36 | PLR, HOZ |
| 2 | 77 | 0.77 | 0.99 | 22 | empty |
| 3 | 71 | 0.76 | 0.99 | 22 | empty |
| 4 | 428 | 0.75 | 0.84 | 56 | PLR |
| 5 | 183 | 0.74 | 0.91 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4335 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
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 Q31QJ2
- Elsewhere: RCSB PDB 3USF · PDBe 3USF · UniProt Q31QJ2
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