Research workbench
Crystal structure of peptidoglycan recognition protein-le in complex with tracheal cytotoxin (monomeric diaminopimelic acid-type peptidoglycan)
Analyse Crystal structure of peptidoglycan recognition protein-le in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CB3
- Type
- protein
- Length
- 682 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan-recognition protein-le
- UniProt
- Q9VXN9
- Ligands
- MLD
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Peptidoglycan-recognition protein-le | protein | 170 | 31% helix, 19% strand | Q9VXN9 |
| B | Peptidoglycan-recognition protein-le | protein | 169 | 31% helix, 20% strand | Q9VXN9 |
| C | Peptidoglycan-recognition protein-le | protein | 173 | 32% helix, 19% strand | Q9VXN9 |
Ligands and binding sites
- MLD · Glcnac(beta1-4)-murnac(1,6-anhydro)-L-ala-gamma-D-glu-meso-A2PM-D-ala · ligand · 4 copies · chains A, B, D, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.80 | 0.83 | 61 | MLD |
| 2 | 721 | 0.78 | 0.83 | 59 | MLD |
| 3 | 297 | 0.62 | 0.79 | 30 | MLD |
| 4 | 151 | 0.46 | 0.77 | 28 | empty |
| 5 | 101 | 0.43 | 0.78 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 665 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 665 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 648 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 133 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 122 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2CB3 · Crystal structure of peptidoglycan recognition protein-LE in complex with tracheal… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9VXN9 · AlphaFold monomer V2.0 prediction for peptidoglycan-recognition protein le (Q9VXN9) · 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 Q9VXN9
- Elsewhere: RCSB PDB 2CB3 · PDBe 2CB3 · UniProt Q9VXN9
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