MolNFT v1 · #118619 · protein
Blood group antigen binding adhesin baba of helicobacter pylori strain 17875 in complex with nanobody nb-ER14
5F7L · Adhesin binding fucosylated histo-blood group antigen: “Blood group antigen binding adhesin baba of helicobacter pylori strain 17875 in complex with nanobody nb-ER14”. X-ray diffraction, 1 ligand (SO4), 15 pockets (best druggability…
- PDB
- 5F7L
- Type
- protein
- Length
- 995 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adhesin binding fucosylated histo-blood group antigen; Nanobody nb-ER14
- UniProt
- O52269
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adhesin binding fucosylated histo-blood group antigen | protein | 375 | 47% helix, 18% strand | O52269 |
| B | Nanobody nb-ER14 | protein | 121 | 10% helix, 53% strand | — |
| C | Adhesin binding fucosylated histo-blood group antigen | protein | 375 | 48% helix, 18% strand | O52269 |
| D | Nanobody nb-ER14 | protein | 124 | 10% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.80 | 0.82 | 78 | empty |
| 2 | 226 | 0.63 | 0.82 | 27 | empty |
| 3 | 215 | 0.57 | 0.80 | 41 | empty |
| 4 | 138 | 0.50 | 0.80 | 24 | empty |
| 5 | 77 | 0.47 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1216 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1024 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5F7L · Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 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
- Elsewhere: RCSB PDB 5F7L · PDBe 5F7L · UniProt O52269
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