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
- 5KR3
- Type
- protein
- Length
- 916 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-aminobutyrate transaminase
- EC
- 2.6.1.18
- Ligands
- PLP
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-aminobutyrate transaminase (EC 2.6.1.18) | protein | 458 | 45% helix, 18% strand | — |
| B | 4-aminobutyrate transaminase (EC 2.6.1.18) | protein | 458 | 45% helix, 18% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.75 | 0.82 | 64 | PLP |
| 2 | 642 | 0.74 | 0.81 | 79 | PLP |
| 3 | 109 | 0.41 | 0.76 | 16 | empty |
| 4 | 111 | 0.38 | 0.74 | 24 | empty |
| 5 | 68 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 5550 Ų buried · 83 hydrogen bonds · protein-protein
Compared structures
- 5KR3 · Directed Evolution of Transaminases By Ancestral Reconstruction. Using Old Proteins for… · 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
- Elsewhere: RCSB PDB 5KR3 · PDBe 5KR3
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