MolNFT v1 · #59886 · protein
Crystal structure of lysn, alpha-aminoadipate aminotransferase, from thermus thermophilus HB27
3CBF · Alpha-aminodipate aminotransferase: “Crystal structure of lysn, alpha-aminoadipate aminotransferase, from thermus thermophilus HB27”. X-ray diffraction, 1 ligand (N5F), 7 pockets (best druggability 0.80). MolNFT v1 #59886 on…
- PDB
- 3CBF
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-aminodipate aminotransferase
- EC
- 2.6.1.39
- UniProt
- Q72LL6
- Ligands
- N5F
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-aminodipate aminotransferase (EC 2.6.1.39) | protein | 392 | 49% helix, 16% strand | Q72LL6 |
Ligands and binding sites
- N5F · (2S)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]hexanedioic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.80 | 0.97 | 29 | N5F |
| 2 | 123 | 0.79 | 0.97 | 34 | N5F |
| 3 | 90 | 0.59 | 0.87 | 18 | empty |
| 4 | 172 | 0.47 | 0.75 | 29 | empty |
| 5 | 159 | 0.44 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3704 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 3CBF · Crystal structure of LysN, alpha-aminoadipate aminotransferase, from Thermus thermophilus… · the same entry in another collection · chain B against B, TM-score 1.00
- Q72LL6 · AlphaFold monomer V2.0 prediction for 2-aminoadipate transaminase (Q72LL6) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 3CBF · PDBe 3CBF · UniProt Q72LL6
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