Research workbench
Directed evolution of transaminases by ancestral reconstruction. using old proteins for new chemistries
Analyse Directed evolution of transaminases by ancestral reconstruction. using old… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KQU
- Type
- protein
- Length
- 2,747 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-aminobutyrate transaminase
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | 4-aminobutyrate transaminase | protein | 457 | 45% helix, 18% strand | — |
| B | 4-aminobutyrate transaminase | protein | 458 | 45% helix, 18% strand | — |
| C, F | 4-aminobutyrate transaminase | protein | 459 | 44% helix, 18% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.76 | 0.79 | 108 | empty |
| 2 | 981 | 0.71 | 0.76 | 81 | empty |
| 3 | 61 | 0.71 | 0.97 | 23 | PLP |
| 4 | 56 | 0.71 | 0.98 | 22 | PLP |
| 5 | 54 | 0.70 | 0.98 | 22 | PLP |
Interfaces
6 interfaces between chains.
- B–C · 5607 Ų buried · 80 hydrogen bonds · protein-protein
- A–D · 5523 Ų buried · 80 hydrogen bonds · protein-protein
- E–F · 5521 Ų buried · 82 hydrogen bonds · protein-protein
- A–C · 485 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 258 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5KQU · Directed Evolution of Transaminases By Ancestral Reconstruction. Using Old Proteins for… · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 5KQU · PDBe 5KQU
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.