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Prephenate dehydrogenase from soybean

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

PDB: 5WHX
Type: protein
Length: 503 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: 3 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prephenate dehydrogenase 1 (EC 1.3.1.13)	protein	250	48% helix, 16% strand	I1MYY4
B	Prephenate dehydrogenase 1 (EC 1.3.1.13)	protein	253	49% helix, 15% strand	I1MYY4

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
CIT · Citric acid · additive · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	489	0.73	0.82	56	NAP, CIT
2	445	0.73	0.83	49	NAP, CIT
3	55	0.28	0.74	10	empty

Interfaces

1 interface between chains.

A–B · 2468 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5WHX · 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 5WHX · PDBe 5WHX · UniProt I1MYY4

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