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Prephenate dehydrogenase N222D mutant from soybean

Analyse Prephenate dehydrogenase N222D mutant from soybean in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T9F
Type: protein
Length: 502 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prephenate dehydrogenase 1
EC: 1.3.1.13
UniProt: I1MYY4
Ligands: NAP, TYR
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prephenate dehydrogenase 1 (EC 1.3.1.13)	protein	249	50% helix, 16% strand	I1MYY4
B	Prephenate dehydrogenase 1 (EC 1.3.1.13)	protein	253	51% helix, 15% strand	I1MYY4

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
TYR · Tyrosine · 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	830	0.74	0.78	86	NAP, TYR
2	453	0.71	0.81	46	NAP, TYR

Interfaces

1 interface between chains.

A–B · 382 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5T9F · Prephenate Dehydrogenase N222D mutant from Soybean · 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 I1MYY4
Elsewhere: RCSB PDB 5T9F · PDBe 5T9F · UniProt I1MYY4

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