MolNFT v1 · #118669 · protein
Blood group antigen binding adhesin baba of helicobacter pylori strain A730 in complex with blood group H lewis B hexasaccharide
5F93 · Adhesin binding fucosylated histo-blood group antigen…: “Blood group antigen binding adhesin baba of helicobacter pylori strain A730 in complex with blood group H…”. X-ray diffraction, 4 ligands (GAL, FUC, GLC), 20 pockets (best…
- PDB
- 5F93
- Type
- protein
- Length
- 2,148 residues
- Chains
- 8
- 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, Q6DSX7
- Ligands
- GAL, FUC, GLC, NAG
- Pockets
- 20 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 18% 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 | 424 | 47% helix, 17% strand | O52269, Q6DSX7 |
| B | Adhesin binding fucosylated histo-blood group antigen, ADHESIN,ADHESIN binding fucosylated histo-blood group antigen | protein | 426 | 46% helix, 17% strand | O52269, Q6DSX7 |
| E | Adhesin binding fucosylated histo-blood group antigen, ADHESIN,ADHESIN binding fucosylated histo-blood group antigen | protein | 420 | 47% helix, 14% strand | O52269, Q6DSX7 |
| G | Adhesin binding fucosylated histo-blood group antigen, ADHESIN,ADHESIN binding fucosylated histo-blood group antigen | protein | 422 | 47% helix, 15% strand | O52269, Q6DSX7 |
| C, D, F, H | Nanobody nb-ER19 | protein | 114 | 6% helix, 48% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B, E, G
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, B, E, G
- GLC · alpha-D-glucopyranose · sugar · 4 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.56 | 0.75 | 40 | empty |
| 2 | 218 | 0.53 | 0.77 | 25 | empty |
| 3 | 229 | 0.53 | 0.76 | 27 | empty |
| 4 | 199 | 0.53 | 0.78 | 23 | empty |
| 5 | 227 | 0.50 | 0.75 | 31 | empty |
Interfaces
9 interfaces between chains.
- G–H · 1069 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 997 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 995 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 990 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 198 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5F93 · Blood group antigen binding adhesin BabA of Helicobacter pylori strain A730 in complex… · the same entry in another collection · chain C against C, 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 Q6DSX7
- Elsewhere: RCSB PDB 5F93 · PDBe 5F93 · UniProt O52269 · UniProt Q6DSX7
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