Research workbench
Crystal structure of lysn, alpha-aminoadipate aminotransferase (substrate free form), from thermus thermophilus HB27
Analyse Crystal structure of lysn, alpha-aminoadipate aminotransferase (substrate free… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EGY
- Type
- protein
- Length
- 1,573 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-aminodipate aminotransferase
- EC
- 2.6.1.39
- UniProt
- Q72LL6
- Ligands
- PLP
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-aminodipate aminotransferase (EC 2.6.1.39) | protein | 392 | 46% helix, 15% strand | Q72LL6 |
| B | Alpha-aminodipate aminotransferase (EC 2.6.1.39) | protein | 394 | 46% helix, 15% strand | Q72LL6 |
| C | Alpha-aminodipate aminotransferase (EC 2.6.1.39) | protein | 396 | 45% helix, 15% strand | Q72LL6 |
| D | Alpha-aminodipate aminotransferase (EC 2.6.1.39) | protein | 391 | 47% helix, 15% strand | Q72LL6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.88 | 0.89 | 108 | PLP |
| 2 | 324 | 0.76 | 0.87 | 46 | empty |
| 3 | 608 | 0.76 | 0.82 | 58 | empty |
| 4 | 587 | 0.75 | 0.82 | 54 | empty |
| 5 | 310 | 0.66 | 0.82 | 39 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3475 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3380 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 1191 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 235 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2EGY · Crystal structure of LysN, alpha-aminoadipate aminotransferase (substrate free form)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q72LL6 · AlphaFold monomer V2.0 prediction for 2-aminoadipate transaminase (Q72LL6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q72LL6
- Elsewhere: RCSB PDB 2EGY · PDBe 2EGY · UniProt Q72LL6
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