MolNFT v1 · #16673 · protein

Crystal structure of a plp-dependent enzyme with plp

1O61 · Aminotransferase: “Crystal structure of a plp-dependent enzyme with plp”. X-ray diffraction, 1 ligand (PLP), 3 pockets (best druggability 0.87). MolNFT v1 #16673 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1O61
Type: protein
Length: 742 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminotransferase
UniProt: Q9S5Y7
Ligands: PLP
Pockets: 3 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aminotransferase	protein	374	40% helix, 18% strand	Q9S5Y7
B	Aminotransferase	protein	368	40% helix, 18% strand	Q9S5Y7

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
ACT · Acetate ion · additive · 5 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1023	0.87	0.88	148	PLP
2	66	0.28	0.73	14	empty
3	70	0.28	0.72	10	empty

Interfaces

1 interface between chains.

A–B · 2724 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

1O61 · Crystal structure of a PLP-dependent enzyme with PLP · 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 Q9S5Y7
Elsewhere: RCSB PDB 1O61 · PDBe 1O61 · UniProt Q9S5Y7

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