MolNFT v1 · #126479 · protein

Alpha-amino epsilon-caprolactam racemase in complex with plp and D/L alpha amino epsilon-caprolactam (internal aldimine)

5M49 · Aminotransferase class-III: “Alpha-amino epsilon-caprolactam racemase in complex with plp and D/L alpha amino epsilon-caprolactam…”. X-ray diffraction, 1 ligand (PLP), 3 pockets (best druggability 0.57). MolNFT v1 #126479 on…

PDB: 5M49
Type: protein
Length: 425 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminotransferase class-III
UniProt: N6UXY4
Ligands: PLP
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aminotransferase class-III	protein	425	40% helix, 18% strand	N6UXY4

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	361	0.57	0.75	46	PLP
2	205	0.57	0.79	26	empty
3	128	0.42	0.76	25	empty

Modifications

Observed in the structure: 2 modified, 1 cofactor (nonstandard, pyridoxal phosphate Schiff base).

Compared structures

5M49 · Alpha-amino epsilon-caprolactam racemase in complex with PLP and D/L alpha amino… · 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 N6UXY4
Elsewhere: RCSB PDB 5M49 · PDBe 5M49 · UniProt N6UXY4

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