MolNFT v1 · #118618 · protein
Blood group antigen binding adhesin baba of helicobacter pylori strain 17875 in complex with nanobody nb-ER19
5F7K · Adhesin binding fucosylated histo-blood group antigen: “Blood group antigen binding adhesin baba of helicobacter pylori strain 17875 in complex with nanobody nb-ER19”. X-ray diffraction, 2 ligands (NA, PO4), 12 pockets (best…
- PDB
- 5F7K
- Type
- protein
- Length
- 1,068 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-ER19
- UniProt
- O52269
- Ligands
- NA, PO4
- Pockets
- 12 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adhesin binding fucosylated histo-blood group antigen | protein | 420 | 49% helix, 15% strand | O52269 |
| C | Nanobody nb-ER19 | protein | 113 | 6% helix, 49% strand | — |
| B | Adhesin binding fucosylated histo-blood group antigen | protein | 421 | 48% helix, 15% strand | O52269 |
| D | Nanobody nb-ER19 | protein | 114 | 6% helix, 48% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, C
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.53 | 0.77 | 27 | empty |
| 2 | 217 | 0.51 | 0.76 | 31 | empty |
| 3 | 196 | 0.50 | 0.76 | 27 | empty |
| 4 | 146 | 0.44 | 0.76 | 24 | empty |
| 5 | 117 | 0.40 | 0.75 | 27 | NA |
Interfaces
3 interfaces between chains.
- A–C · 979 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 972 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 498 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5F7K · 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 5F7K · PDBe 5F7K · UniProt O52269
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