Research workbench
Blood group antigen binding adhesin baba of helicobacter pylori strain S831 in complex with blood group H lewis B hexasaccharide
Analyse Blood group antigen binding adhesin baba of helicobacter pylori strain S831 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F8R
- Type
- protein
- Length
- 1,065 residues
- Chains
- 4
- 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, Q6DSZ5
- Ligands
- GAL, FUC, BGC, NAG
- Pockets
- 16 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 40% 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 | 49% helix, 16% strand | O52269, Q6DSZ5 |
| B | Adhesin binding fucosylated histo-blood group antigen, ADHESIN,ADHESIN binding fucosylated histo-blood group antigen | protein | 421 | 48% helix, 16% strand | O52269, Q6DSZ5 |
| C | Nanobody nb-ER19 | protein | 113 | 6% helix, 47% strand | — |
| D | Nanobody nb-ER19 | protein | 114 | 6% helix, 48% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.54 | 0.77 | 27 | empty |
| 2 | 175 | 0.49 | 0.76 | 28 | empty |
| 3 | 141 | 0.47 | 0.77 | 15 | empty |
| 4 | 134 | 0.46 | 0.77 | 23 | empty |
| 5 | 114 | 0.40 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1000 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 985 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 516 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5F8R · Blood group antigen binding adhesin BabA of Helicobacter pylori strain S831 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 Q6DSZ5
- Elsewhere: RCSB PDB 5F8R · PDBe 5F8R · UniProt O52269 · UniProt Q6DSZ5
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