Research workbench
Crystal structure of the complex of camel peptidoglycan recognition protein with disaccharide at 3.2A resolution
Analyse Crystal structure of the complex of camel peptidoglycan recognition protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R2K
- Type
- protein
- Length
- 684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan recognition protein
- UniProt
- Q9GK12
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein | protein | 171 | 25% helix, 20% strand | Q9GK12 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 5 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.84 | 0.85 | 127 | TLA |
| 2 | 55 | 0.37 | 0.79 | 20 | empty |
| 3 | 75 | 0.30 | 0.73 | 20 | empty |
| 4 | 58 | 0.25 | 0.72 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 788 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 559 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 366 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 93 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 80 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2R2K · Crystal structure of the complex of camel peptidoglycan recognition protein with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GK12 · AlphaFold monomer V2.0 prediction for peptidoglycan recognition protein 1 (Q9GK12) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9GK12
- Elsewhere: RCSB PDB 2R2K · PDBe 2R2K · UniProt Q9GK12
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