MolNFT v2 · #117336 · protein
Crystal structure of the complex of Peptidoglycan recognition protein, PGRP-S from camel with ethylene glycol at 1.83 A resolution
5DWF · Peptidoglycan recognition protein 1: “Crystal structure of the complex of Peptidoglycan recognition protein, PGRP-S from camel with ethylene glycol…”. X-ray diffraction at 1.83, 3 pockets (best druggability 0.79). MolNFT v2 #117336…
- PDB
- 5DWF
- Type
- protein
- Length
- 664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.83
- Source
- Camelus dromedarius
- Molecule
- Peptidoglycan recognition protein 1
- UniProt
- Q9GK12
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.83 · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 166 | 35% helix, 20% strand | Q9GK12 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, A, D
- TLA · L(+)-tartaric acid · additive · chains C, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.79 | 0.81 | 113 | TLA, GOL, EDO |
| 2 | 83 | 0.31 | 0.73 | 21 | empty |
| 3 | 50 | 0.25 | 0.73 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 662 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 522 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 372 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5DWF · Crystal structure of the complex of peptidoglycan recognition protein, pgrp-S from camel… · 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 5DWF · PDBe 5DWF · UniProt Q9GK12
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