Research workbench
Crystal structure of tcda-A2 bound to A20.1 vhh and A26.8 vhh
Analyse Crystal structure of tcda-A2 bound to A20.1 vhh and A26.8 vhh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NC1
- Type
- protein
- Length
- 954 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell wall-binding repeat protein; A20.1 vhh; A26.8 vhh
- UniProt
- D5RWT1
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell wall-binding repeat protein | protein | 214 | 0% helix, 48% strand | D5RWT1 |
| C | A20.1 vhh | protein | 123 | 5% helix, 51% strand | — |
| E | A26.8 vhh | protein | 124 | 9% helix, 48% strand | — |
| B | Cell wall-binding repeat protein | protein | 248 | 0% helix, 50% strand | D5RWT1 |
| D | A20.1 vhh | protein | 122 | 5% helix, 50% strand | — |
| F | A26.8 vhh | protein | 123 | 5% helix, 47% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.76 | 0.79 | 105 | empty |
| 2 | 572 | 0.71 | 0.79 | 65 | empty |
| 3 | 63 | 0.42 | 0.81 | 14 | empty |
| 4 | 66 | 0.34 | 0.76 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–C · 827 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 806 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 541 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 518 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4NC1 · Crystal Structure of TcdA-A2 Bound to A20.1 VHH and A26.8 VHH · 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 D5RWT1
- Elsewhere: RCSB PDB 4NC1 · PDBe 4NC1 · UniProt D5RWT1
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