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Blood group antigen binding adhesin baba of helicobacter pylori strain A730 in complex with blood group a type 1 hexasaccharide
Analyse Blood group antigen binding adhesin baba of helicobacter pylori strain A730 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F97
- Type
- protein
- Length
- 2,160 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, BGC, NAG, FUC, A2G
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Adhesin binding fucosylated histo-blood group antigen, ADHESIN,ADHESIN binding fucosylated histo-blood group antigen | protein | 426 | 47% helix, 15% strand | O52269, Q6DSX7 |
| E, G | Nanbody nb-ER19 | protein | 114 | 9% helix, 47% strand | — |
| F | Nanbody nb-ER19 | protein | 115 | 9% helix, 48% strand | — |
| H | Nanbody nb-ER19 | protein | 113 | 6% helix, 48% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.69 | 0.78 | 77 | empty |
| 2 | 681 | 0.65 | 0.74 | 73 | empty |
| 3 | 224 | 0.55 | 0.78 | 28 | empty |
| 4 | 216 | 0.53 | 0.77 | 26 | empty |
| 5 | 199 | 0.52 | 0.77 | 24 | empty |
Interfaces
11 interfaces between chains.
- D–H · 1005 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 998 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 993 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 989 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 596 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5F97 · Blood group antigen binding adhesin BabA of Helicobacter pylori strain A730 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 Q6DSX7
- Elsewhere: RCSB PDB 5F97 · PDBe 5F97 · UniProt O52269 · UniProt Q6DSX7
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