Research workbench
Adenylate cyclase toxin rtx domain fragment bound to M1H5 Fab and M2B10 Fab
Analyse Adenylate cyclase toxin rtx domain fragment bound to M1H5 Fab and M2B10 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RAH
- Type
- protein
- Length
- 1,182 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M1H5 Fab light chain; M1H5 Fab heavy chain; M2B10 Fab light chain; M2B10 Fab heavy chain…
- UniProt
- A0A380ZZA1
- Ligands
- CA, PO4
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1H5 Fab light chain | protein | 215 | 6% helix, 52% strand | — |
| B | M1H5 Fab heavy chain | protein | 223 | 9% helix, 53% strand | — |
| C | M2B10 Fab light chain | protein | 185 | 5% helix, 46% strand | — |
| D | M2B10 Fab heavy chain | protein | 199 | 5% helix, 49% strand | — |
| E | Bifunctional adenylate cyclase TOXIN/HEMOLYSIN cyaa, bifunctional adenylate cyclase TOXIN/HEMOLYSIN cyaa | protein | 360 | 4% helix, 39% strand | A0A380ZZA1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.70 | 0.78 | 60 | empty |
| 2 | 349 | 0.58 | 0.76 | 47 | empty |
| 3 | 319 | 0.52 | 0.73 | 47 | empty |
| 4 | 51 | 0.46 | 0.85 | 19 | empty |
| 5 | 70 | 0.44 | 0.82 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2036 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1526 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 881 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 649 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 285 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7RAH · Adenylate cyclase toxin RTX domain fragment bound to M1H5 Fab and M2B10 Fab · 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 A0A380ZZA1
- Elsewhere: RCSB PDB 7RAH · PDBe 7RAH · UniProt A0A380ZZA1
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