MolNFT v1 · #138543 · protein

Arabidopsis thaliana prephenate aminotransferase

5WMH · Bifunctional aspartate aminotransferase and…: “Arabidopsis thaliana prephenate aminotransferase”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.81). MolNFT v1 #138543 on GenesisL1: 3D structure, binding sites…

PDB: 5WMH
Type: protein
Length: 2,395 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate…
EC: 2.6.1.1, 2.6.1.78, 2.6.1.79
UniProt: Q9SIE1
Ligands: PLP
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate aminotransferase (EC 2.6.1.1, 2.6.1.78, 2.6.1.79)	protein	399	43% helix, 13% strand	Q9SIE1
C	Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate aminotransferase (EC 2.6.1.1, 2.6.1.78, 2.6.1.79)	protein	401	44% helix, 12% strand	Q9SIE1
D	Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate aminotransferase (EC 2.6.1.1, 2.6.1.78, 2.6.1.79)	protein	400	40% helix, 13% strand	Q9SIE1
F	Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate aminotransferase (EC 2.6.1.1, 2.6.1.78, 2.6.1.79)	protein	397	36% helix, 11% strand	Q9SIE1

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	954	0.81	0.83	104	PLP
2	717	0.81	0.84	72	PLP
3	931	0.77	0.80	89	PLP
4	782	0.75	0.80	65	empty
5	832	0.75	0.79	71	PLP

Interfaces

6 interfaces between chains.

C–D · 2844 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 2624 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 2599 Å² buried · 42 hydrogen bonds · protein-protein
B–F · 519 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 242 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5WMH · Arabidopsis thaliana prephenate aminotransferase · the same entry in another collection · chain F against F, TM-score 1.00
Q9SIE1 · AlphaFold monomer V2.0 prediction for bifunctional aspartate aminotransferase and… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9SIE1
Elsewhere: RCSB PDB 5WMH · PDBe 5WMH · UniProt Q9SIE1

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