Research workbench
Ricin bound to vhh antibody V6E11
Analyse Ricin bound to vhh antibody V6E11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KBK
- Type
- protein
- Length
- 643 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin; Vhh antibody V6E11
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- NAG, BMA, FUC, CL, SO4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin (EC 3.2.2.22) | protein | 258 | 40% helix, 23% strand | P02879 |
| B | Ricin (EC 3.2.2.22) | protein | 261 | 13% helix, 36% strand | P02879 |
| C | Vhh antibody V6E11 | protein | 124 | 5% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · chains A
- CL · Chloride ion · ion · 7 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.79 | 0.92 | 41 | empty |
| 2 | 375 | 0.69 | 0.82 | 50 | empty |
| 3 | 160 | 0.60 | 0.83 | 32 | empty |
| 4 | 211 | 0.53 | 0.77 | 30 | empty |
| 5 | 177 | 0.51 | 0.78 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1670 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 454 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 209 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7KBK · Ricin bound to VHH antibody V6E11 · 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 P02879
- Elsewhere: RCSB PDB 7KBK · PDBe 7KBK · UniProt P02879
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