Research workbench
Structure of fucosylated D-antimicrobial peptide SB10 in complex with the fucose-binding lectin pa-iil at 1.707 ångström resolution
Analyse Structure of fucosylated D-antimicrobial peptide SB10 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
- 6Q8H
- Type
- protein
- Length
- 138 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; SB10
- UniProt
- A0A069Q9V4
- Ligands
- DLE, ZDC, CA, NH2
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| B, C | SB10 | protein | 12 | 83% helix, 0% strand | — |
Ligands and binding sites
- DLE · D-leucine · ligand · 2 copies · chains A, B, C
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 2 copies · chains A, B, C
- CA · Calcium ion · metal · 2 copies · chains A
- NH2 · Amino group · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.35 | 0.74 | 18 | ZDC |
Interfaces
3 interfaces between chains.
- B–C · 251 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 103 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 d-amino, 2 covalent (D-amino acid, covalent ligand).
Compared structures
- 6Q8H · Structure of Fucosylated D-antimicrobial peptide SB10 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 6Q8H · PDBe 6Q8H · UniProt A0A069Q9V4
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