Research workbench
Crystal structure of the ectodomain of drosophila transmembrane receptor pgrp-lca
Analyse Crystal structure of the ectodomain of drosophila transmembrane receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z6I
- Type
- protein
- Length
- 167 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan-recognition protein-lc
- UniProt
- Q9GNK5
- Ligands
- NAG, SO4
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan-recognition protein-lc | protein | 167 | 29% helix, 20% strand | Q9GNK5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.39 | 0.77 | 20 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1Z6I · Crystal structure of the ectodomain of Drosophila transmembrane receptor PGRP-LCa · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GNK5 · AlphaFold monomer V2.0 prediction for peptidoglycan-recognition protein lc (Q9GNK5) · 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 Q9GNK5
- Elsewhere: RCSB PDB 1Z6I · PDBe 1Z6I · UniProt Q9GNK5
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