Research workbench
Structure of fucosylated D-antimicrobial peptide SB8 in complex with the fucose-binding lectin pa-iil at 1.190 ångström resolution
Analyse Structure of fucosylated D-antimicrobial peptide SB8 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q8G
- Type
- protein
- Length
- 480 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; SB8
- UniProt
- A0A069Q9V4
- Ligands
- ZDC, CA, NH2
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| E, F | SB8 | protein | 11 | 73% helix, 0% strand | — |
| G | SB8 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 4 copies · chains A, E, B, F, C, D, G
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- NH2 · Amino group · ion · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.36 | 0.73 | 19 | empty |
| 2 | 111 | 0.35 | 0.73 | 18 | empty |
| 3 | 56 | 0.26 | 0.73 | 17 | ZDC |
Interfaces
9 interfaces between chains.
- C–D · 1332 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1324 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 524 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 225 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 d-amino, 3 glycan (D-amino acid, glycosylation).
Compared structures
- 6Q8G · Structure of Fucosylated D-antimicrobial peptide SB8 in complex with the Fucose-binding… · 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 6Q8G · PDBe 6Q8G · UniProt A0A069Q9V4
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