Research workbench
Blood group antigen binding adhesin baba of helicobacter pylori strain S831 in complex with nanobody nb-ER19
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
- 5F8Q
- 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
- Pockets
- 15 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adhesin binding fucosylated histo-blood group antigen, ADHESIN,ADHESIN binding fucosylated histo-blood group antigen | protein | 419 | 48% helix, 15% strand | O52269, Q6DSZ5 |
| C | Nanobody nb-ER19 | protein | 113 | 6% helix, 48% strand | — |
| D | Nanobody nb-ER19 | protein | 114 | 6% helix, 47% strand | — |
Pockets
15 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.51 | 0.76 | 30 | empty |
| 2 | 166 | 0.49 | 0.77 | 27 | empty |
| 3 | 169 | 0.47 | 0.76 | 23 | empty |
| 4 | 119 | 0.43 | 0.77 | 15 | empty |
| 5 | 99 | 0.40 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 986 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 978 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 528 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5F8Q · 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 5F8Q · PDBe 5F8Q · UniProt O52269 · UniProt Q6DSZ5
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