MolNFT v1 · #170231 · protein
Fucosylated antimicrobial peptide SB6 in complex with the lectin lecrsl from ralstonia solanacearum at 2.4 ångström resolution
6Y0X · Fucose-binding lectin protein: “Fucosylated antimicrobial peptide SB6 in complex with the lectin lecrsl from ralstonia solanacearum at 2.4…”. X-ray diffraction, 3 ligands (DLY, ZDC, NH2), 10 pockets (best druggability 0.75). MolNFT…
- 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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