Research workbench
Cfucosylated second generation peptide dendrimer SBD6 bound to fucose binding lectin lecb (pa-iil) from pseudomonas aeruginosa at 2.08 ångström resolution, incomplete structure
Analyse Cfucosylated second generation peptide dendrimer SBD6 bound to fucose binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S5R
- Type
- protein
- Length
- 459 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; SBD6
- UniProt
- A0A069Q9V4
- Ligands
- DPP, ZDC, CA
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 69% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| H | SBD6 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- DPP · Diaminopropanoic acid · ligand · chains B
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 4 copies · chains A, B, C, D, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.37 | 0.78 | 19 | empty |
| 2 | 123 | 0.36 | 0.72 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1314 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1279 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 457 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 135 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 d-amino, 1 glycan, 1 modified (D-amino acid, glycosylation, nonstandard).
Compared structures
- 6S5R · Cfucosylated second generation peptide dendrimer SBD6 bound to Fucose binding Lectin LecB… · 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 A0A069Q9V4
- Elsewhere: RCSB PDB 6S5R · PDBe 6S5R · UniProt A0A069Q9V4
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