MolNFT v1 · #163527 · protein
Cfucosylated peptide SBL2 bound to fucose binding lectin lecb (pa-iil) from pseudomonas aeruginosa at 1.46 ångström resolution
6S5P · Fucose-binding lectin: “Cfucosylated peptide SBL2 bound to fucose binding lectin lecb (pa-iil) from pseudomonas aeruginosa at 1.46…”. X-ray diffraction, 3 ligands (ZDC, CA, NH2), 3 pockets (best druggability 0.32). MolNFT v1 #163527…
- PDB
- 6S5P
- Type
- protein
- Length
- 464 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; SBL2
- UniProt
- A0A069Q9V4
- Ligands
- ZDC, CA, NH2
- Pockets
- 3 · best druggability 0.32
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 67% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| H | SBL2 | protein | 6 | 0% helix, 0% strand | — |
| E, F | SBL2 | protein | 1 | 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, B, E, F, C, D, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- NH2 · Amino group · ion · chains H
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 | 93 | 0.32 | 0.73 | 18 | empty |
| 2 | 93 | 0.31 | 0.72 | 18 | empty |
| 3 | 55 | 0.26 | 0.74 | 19 | ZDC |
Interfaces
9 interfaces between chains.
- A–B · 1334 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1330 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 526 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (glycosylation).
Compared structures
- 6S5P · Cfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas… · 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 6S5P · PDBe 6S5P · UniProt A0A069Q9V4
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