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Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant pseudomonas aeruginosa
Analyse Discovery, crystal structures and atomic force microscopy study of thioether… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NES
- Type
- protein
- Length
- 467 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin II (pa-iil); Cyd-TRP-trd-lys-lyd-lys-lyd-lys-trd-TRP-cyd
- UniProt
- A0A069Q9V4
- Ligands
- 8VH, ZDC, CA
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin II (pa-iil) | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| E | Cyd-TRP-trd-lys-lyd-lys-lyd-lys-trd-TRP-cyd | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- 8VH · 1,3-dimethylbenzene · ligand · chains E
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 4 copies · chains A, C, E, B, D
- CA · Calcium ion · metal · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.33 | 0.73 | 19 | empty |
| 2 | 104 | 0.33 | 0.72 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1354 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1354 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 521 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 246 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 d-amino, 2 covalent, 1 glycan (D-amino acid, covalent ligand, glycosylation).
Compared structures
- 5NES · Discovery, crystal structures and atomic force microscopy study of thioether ligated… · 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 A0A069Q9V4
- Elsewhere: RCSB PDB 5NES · PDBe 5NES · UniProt A0A069Q9V4
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