Research workbench
Crystal structure of peptidoglycan-associated outer membrane lipoprotein from Yersinia pestis CO92
Analyse Crystal structure of peptidoglycan-associated outer membrane lipoprotein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PWT
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.752
- Source
- Yersinia pestis
- Molecule
- Peptidoglycan-associated lipoprotein
- UniProt
- Q7CH55
- Ligands
- POP, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.752 · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidoglycan-associated lipoprotein | protein | 130 | 48% helix, 16% strand | Q7CH55 |
| C | Peptidoglycan-associated lipoprotein | protein | 123 | 48% helix, 15% strand | Q7CH55 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C, A
- FMT · Formic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.65 | 0.80 | 36 | empty |
| 2 | 365 | 0.61 | 0.77 | 36 | POP |
| 3 | 65 | 0.29 | 0.74 | 13 | SO4 |
| 4 | 73 | 0.29 | 0.73 | 20 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 486 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 204 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 139 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4PWT · Crystal structure of peptidoglycan-associated outer membrane lipoprotein from yersinia… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7CH55
- Elsewhere: RCSB PDB 4PWT · PDBe 4PWT · UniProt Q7CH55
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