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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: 5KR4
Type: protein
Length: 914 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-aminobutyrate transaminase
Ligands: PLP
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	4-aminobutyrate transaminase	protein	457	45% helix, 18% strand	—

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.74	0.80	75	PLP, EDO
2	597	0.72	0.80	66	PLP
3	114	0.43	0.77	20	empty
4	77	0.38	0.78	17	empty
5	88	0.34	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 5446 Å² buried · 83 hydrogen bonds · protein-protein

Compared structures

5KR4 · 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 5KR4 · PDBe 5KR4

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