MolNFT v1 · #111936 · protein

The plant peptide hormone receptor

4Z5W · Phytosulfokine receptor 1: “The plant peptide hormone receptor”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.61). MolNFT v1 #111936 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Z5W
Type: protein
Length: 1,207 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phytosulfokine receptor 1; Phytosulfokine
EC: 2.7.11.1
UniProt: Q8LPB4
Ligands: NAG
Pockets: 7 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phytosulfokine receptor 1 (EC 2.7.11.1)	protein	596	17% helix, 21% strand	Q8LPB4
B	Phytosulfokine receptor 1 (EC 2.7.11.1)	protein	601	17% helix, 23% strand	Q8LPB4
P, Q	Phytosulfokine	protein	5	0% helix, 40% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains B, A, Q, P

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	362	0.61	0.77	51	empty
2	225	0.55	0.78	39	empty
3	122	0.46	0.78	25	empty
4	187	0.45	0.74	28	empty
5	93	0.42	0.79	20	empty

Interfaces

3 interfaces between chains.

A–B · 997 Å² buried · 8 hydrogen bonds · protein-protein
A–Q · 757 Å² buried · 16 hydrogen bonds · protein-protein
B–P · 742 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 glycan, 9 disulfide, 4 modified (N-glycosylation, disulfide, sulfation).

Compared structures

4Z5W · The plant peptide hormone receptor · the same entry in another collection · chain A against A, TM-score 1.00
Q8LPB4 · AlphaFold monomer V2.0 prediction for phytosulfokine receptor 1 (Q8LPB4) · 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 Q8LPB4
Elsewhere: RCSB PDB 4Z5W · PDBe 4Z5W · UniProt Q8LPB4

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