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
- 5KQW
- Type
- protein
- Length
- 1,829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-aminobutyrate transaminase
- EC
- 2.6.1.18
- Ligands
- MG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 4-aminobutyrate transaminase (EC 2.6.1.18) | protein | 457 | 45% helix, 18% strand | — |
| B | 4-aminobutyrate transaminase (EC 2.6.1.18) | protein | 458 | 45% helix, 18% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.82 | 0.86 | 101 | empty |
| 2 | 529 | 0.75 | 0.83 | 69 | empty |
| 3 | 692 | 0.74 | 0.80 | 85 | empty |
| 4 | 380 | 0.74 | 0.85 | 61 | empty |
| 5 | 594 | 0.74 | 0.81 | 73 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5559 Ų buried · 80 hydrogen bonds · protein-protein
- C–D · 5542 Ų buried · 78 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 91 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KQW · 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 5KQW · PDBe 5KQW
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