MolNFT v1 · #134613 · protein

Seleno-methionine prephenate dehydrogenase from soybean

5T9E · Prephenate dehydrogenase 1: “Seleno-methionine prephenate dehydrogenase from soybean”. X-ray diffraction, 1 ligand (NAP), 2 pockets (best druggability 0.74). MolNFT v1 #134613 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5T9E
Type: protein
Length: 500 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
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Prephenate dehydrogenase 1 (EC 1.3.1.13)	protein	250	50% helix, 16% strand	I1MYY4

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide 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	482	0.74	0.83	48	NAP
2	441	0.73	0.83	52	NAP

Interfaces

1 interface between chains.

A–B · 2554 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 modified (engineered).

Compared structures

5T9E · Seleno-methionine Prephenate Dehydrogenase 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 5T9E · PDBe 5T9E · UniProt I1MYY4

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