Research workbench
Crystal Structure of the complex of Camel Peptidoglycan Recognition Protein (CPGRP-S) and N-Acetylglucosamine at 2.6 A
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
- 5E0A
- Type
- protein
- Length
- 684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Camelus dromedarius
- Molecule
- Peptidoglycan recognition protein 1
- UniProt
- Q9GK12
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.6 · 1 distinct chain · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 171 | 27% helix, 19% strand | Q9GK12 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, C, D
- TLA · L(+)-tartaric acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.82 | 0.85 | 92 | NAG, TLA |
| 2 | 477 | 0.68 | 0.79 | 41 | empty |
| 3 | 229 | 0.50 | 0.75 | 36 | empty |
| 4 | 56 | 0.31 | 0.76 | 21 | empty |
| 5 | 53 | 0.25 | 0.73 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 764 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 523 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 378 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 101 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 90 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5E0A · Crystal structure of the complex of camel peptidoglycan recognition protein (cpgrp-S) and… · 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 0.99
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 Q9GK12
- Elsewhere: RCSB PDB 5E0A · PDBe 5E0A · UniProt Q9GK12
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