Research workbench
Crystal structure of the lfz ectodomain of the peptidoglycan recognition protein lf
Analyse Crystal structure of the lfz ectodomain of the peptidoglycan recognition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XZ4
- Type
- protein
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan-recognition protein lf
- UniProt
- Q8SXQ7
- Ligands
- 1PG, CU
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan-recognition protein lf | protein | 165 | 27% helix, 20% strand | Q8SXQ7 |
| B | Peptidoglycan-recognition protein lf | protein | 161 | 30% helix, 20% strand | Q8SXQ7 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
- CU · Copper (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.63 | 0.81 | 29 | EDO |
| 2 | 74 | 0.33 | 0.75 | 18 | EDO |
Interfaces
1 interface between chains.
- A–B · 638 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2XZ4 · Crystal structure of the LFZ ectodomain of the peptidoglycan recognition protein LF · the same entry in another collection · chain A against A, TM-score 1.00
- Q8SXQ7 · AlphaFold monomer V2.0 prediction for peptidoglycan-recognition protein lf (Q8SXQ7) · a predicted model of the same protein · chain B 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 Q8SXQ7
- Elsewhere: RCSB PDB 2XZ4 · PDBe 2XZ4 · UniProt Q8SXQ7
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