MolNFT v1 · #118679 · protein
Blood group antigen binding adhesin baba of helicobacter pylori strain P436 in complex with lewis B blood group B heptasaccharide
5F9D · Adhesin binding fucosylated histo-blood group antigen…: “Blood group antigen binding adhesin baba of helicobacter pylori strain P436 in complex with lewis B blood…”. X-ray diffraction, 5 ligands (GAL, FUC, BGC), 8 pockets (best…
- PDB
- 5F9D
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adhesin binding fucosylated histo-blood group antigen, ADHESIN,ADHESIN binding…
- UniProt
- O52269, Q6DT10
- Ligands
- GAL, FUC, BGC, NAG, GLA
- Pockets
- 8 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adhesin binding fucosylated histo-blood group antigen, ADHESIN,ADHESIN binding fucosylated histo-blood group antigen | protein | 417 | 48% helix, 16% strand | O52269, Q6DT10 |
| C | Nanobody nb-ER19 | protein | 114 | 6% helix, 47% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GLA · alpha-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.50 | 0.76 | 28 | empty |
| 2 | 156 | 0.44 | 0.75 | 24 | empty |
| 3 | 101 | 0.37 | 0.74 | 21 | empty |
| 4 | 59 | 0.36 | 0.79 | 15 | empty |
| 5 | 77 | 0.35 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 985 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5F9D · Blood group antigen binding adhesin BabA of Helicobacter pylori strain P436 in complex… · 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 O52269
- Every structure of UniProt Q6DT10
- Elsewhere: RCSB PDB 5F9D · PDBe 5F9D · UniProt O52269 · UniProt Q6DT10
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