Research workbench
Crystal structure of a degt dnrj ERYC1 strs aminotransferase from brucella abortus
Analyse Crystal structure of a degt dnrj ERYC1 strs aminotransferase from brucella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QGR
- Type
- protein
- Length
- 749 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DEGT/DNRJ/ERYC1/STRS aminotransferase
- UniProt
- Q2YRB9
- Ligands
- PLP, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DEGT/DNRJ/ERYC1/STRS aminotransferase | protein | 376 | 42% helix, 16% strand | Q2YRB9 |
| B | DEGT/DNRJ/ERYC1/STRS aminotransferase | protein | 373 | 42% helix, 16% strand | Q2YRB9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.73 | 0.81 | 56 | ACT, PLP |
| 2 | 484 | 0.73 | 0.82 | 58 | PLP, ACT |
| 3 | 88 | 0.48 | 0.82 | 29 | empty |
| 4 | 93 | 0.37 | 0.75 | 19 | empty |
| 5 | 100 | 0.37 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2047 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4QGR · Crystal structure of a DegT DnrJ EryC1 StrS aminotransferase from Brucella abortus · 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 Q2YRB9
- Elsewhere: RCSB PDB 4QGR · PDBe 4QGR · UniProt Q2YRB9
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