Research workbench
Crystal structure of the lfw ectodomain of the peptidoglycan recognition protein lf
Analyse Crystal structure of the lfw 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
- 2XZ8
- Type
- protein
- Length
- 269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan-recognition protein lf
- UniProt
- Q8SXQ7
- Ligands
- NA
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan-recognition protein lf | protein | 135 | 28% helix, 24% strand | Q8SXQ7 |
| B | Peptidoglycan-recognition protein lf | protein | 134 | 28% helix, 25% strand | Q8SXQ7 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.77 | 0.83 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 618 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2XZ8 · Crystal structure of the lfw 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 2XZ8 · PDBe 2XZ8 · UniProt Q8SXQ7
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