Research workbench
Fucosylated antimicrobial peptide SB6 in complex with the lectin lecrsl from ralstonia solanacearum at 2.4 ångström resolution
Analyse Fucosylated antimicrobial peptide SB6 in complex with the lectin lecrsl from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y0X
- Type
- protein
- Length
- 616 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin protein; SB6
- UniProt
- A0A0S4TLR1
- Ligands
- DLY, ZDC, NH2
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Fucose-binding lectin protein | protein | 89 | 0% helix, 69% strand | A0A0S4TLR1 |
| I | SB6 | protein | 5 | 0% helix, 0% strand | — |
| J, L, M, O, Q | SB6 | protein | 12 | 75% helix, 0% strand | — |
| K | SB6 | protein | 6 | 0% helix, 0% strand | — |
| R | SB6 | protein | 11 | 55% helix, 0% strand | — |
Ligands and binding sites
- DLY · D-lysine · ligand · chains A
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 12 copies · chains A, B, I, F, J, C, K, L, D, E, M, O, Q, R
- NH2 · Amino group · ion · 5 copies · chains J, L, M, O, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.75 | 0.81 | 78 | empty |
| 2 | 742 | 0.75 | 0.80 | 76 | empty |
| 3 | 276 | 0.60 | 0.79 | 47 | ZDC |
| 4 | 246 | 0.59 | 0.80 | 35 | empty |
| 5 | 299 | 0.57 | 0.77 | 37 | ZDC |
Interfaces
20 interfaces between chains.
- B–C · 797 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 753 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 750 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 744 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 741 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 82 d-amino, 8 glycan (D-amino acid, glycosylation).
Compared structures
- 6Y0X · Fucosylated antimicrobial peptide SB6 in complex with the lectin LecRSL from Ralstonia… · the same entry in another collection · chain B against B, 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 A0A0S4TLR1
- Elsewhere: RCSB PDB 6Y0X · PDBe 6Y0X · UniProt A0A0S4TLR1
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