MolNFT v1 · #128049 · protein
Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant pseudomonas aeruginosa
5NF0 · Fucose-binding lectin II (pa-iil): “Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial…”. X-ray diffraction, 4 ligands (OXE, ZDC, CA), 5 pockets (best druggability 0.41).…
- PDB
- 5NF0
- Type
- protein
- Length
- 490 residues
- Chains
- 8
- 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-gly…
- UniProt
- A0A069Q9V4
- Ligands
- OXE, ZDC, CA, NH2
- Pockets
- 5 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 64% 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, G, H | Cyd-TRP-trd-lys-lyd-lys-lyd-lys-trd-TRP-cyd-gly | protein | 11 | 0% helix, 0% strand | — |
| F | Fragment of ligand | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- OXE · Ortho-xylene · ligand · 3 copies · chains B, E, D, G, C, H
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 4 copies · chains A, C, F, B, D, E, H, G
- CA · Calcium ion · metal · 8 copies · chains A, C, B, D, G
- NH2 · Amino group · ion · 3 copies · chains E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.41 | 0.83 | 18 | ZDC |
| 2 | 69 | 0.40 | 0.80 | 22 | ZDC, OXE |
| 3 | 72 | 0.36 | 0.77 | 20 | ZDC, OXE |
| 4 | 116 | 0.35 | 0.73 | 18 | empty |
| 5 | 99 | 0.32 | 0.72 | 19 | empty |
Interfaces
13 interfaces between chains.
- A–C · 1353 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1342 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 525 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 523 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 261 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 d-amino, 6 covalent, 4 glycan (D-amino acid, covalent ligand, glycosylation).
Compared structures
- 5NF0 · 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 5NF0 · PDBe 5NF0 · UniProt A0A069Q9V4
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