MolNFT v1 · #37023 · protein

Psec aminotransferase with external aldimine

2FNU: “Psec aminotransferase with external aldimine”. X-ray diffraction, 2 ligands (PMP, UD1), 7 pockets (best druggability 0.76). MolNFT v1 #37023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2FNU
Type: protein
Length: 747 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminotransferase
UniProt: O25130
Ligands: PMP, UD1
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aminotransferase	protein	373	43% helix, 18% strand	O25130
B	Aminotransferase	protein	374	42% helix, 18% strand	O25130

Ligands and binding sites

PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 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	644	0.76	0.82	67	PMP, UD1
2	603	0.74	0.81	60	PMP, UD1
3	167	0.45	0.75	24	empty
4	67	0.37	0.78	10	empty
5	107	0.35	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 2909 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

2FNU · PseC aminotransferase with external aldimine · the same entry in another collection · chain A against A, TM-score 1.00
O25130 · AlphaFold monomer V2.0 prediction for udp-4-amino-4,6-dideoxy-N… · a predicted model of the same protein · 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 O25130
Elsewhere: RCSB PDB 2FNU · PDBe 2FNU · UniProt O25130

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