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Crystal structure of D-amino acid aminotransferase from aminobacterium colombiense in holo form with plp

Analyse Crystal structure of D-amino acid aminotransferase from aminobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8AHR
Type: protein
Length: 542 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminotransferase class IV
UniProt: D5EHC5
Ligands: PLP
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aminotransferase class IV	protein	271	31% helix, 31% strand	D5EHC5

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

2 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	790	0.81	0.84	74	PLP
2	466	0.68	0.80	48	PLP

Interfaces

1 interface between chains.

A–B · 1869 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

8AHR · Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense in… · 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
Every structure of UniProt D5EHC5
Elsewhere: RCSB PDB 8AHR · PDBe 8AHR · UniProt D5EHC5

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