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MolNFT v1 · #121552 · protein

Plant peptide hormone receptor RGFR1 in complex with RGF1

5HYX · Probable lrr receptor-like SERINE/THREONINE-protein kinase…: “Plant peptide hormone receptor RGFR1 in complex with RGF1”. X-ray diffraction, 1 ligand (NAG). MolNFT v1 #121552 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
5HYX
Type
protein
Length
639 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Probable lrr receptor-like SERINE/THREONINE-protein kinase AT4G26540…
EC
2.7.11.1
UniProt
C0LGR3
Ligands
NAG

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BProbable lrr receptor-like SERINE/THREONINE-protein kinase AT4G26540 (EC 2.7.11.1)protein62619% helix, 24% strandC0LGR3
APtr-ser-asn-pro-gly-his-his-pro-hyp-arg-his-asnprotein130% helix, 0% strand—

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B

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

Interfaces

1 interface between chains.

  • B–A · 968 Ų buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan, 2 modified (N-glycosylation, nonstandard, phosphorylation).

Compared structures

  • 5HYX · Plant peptide hormone receptor RGFR1 in complex with RGF1 · the same entry in another collection · chain B against B, TM-score 1.00
  • C0LGR3 · AlphaFold monomer V2.0 prediction for lrr receptor-like SERINE/THREONINE-protein kinase… · a predicted model of the same protein · chain B against A, TM-score 0.98

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