Research workbench
Ricin bound to vhh antibody V11B2
Analyse Ricin bound to vhh antibody V11B2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KD2
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin chain a; Ricin chain B; Vhh antibody V11B2
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- NAG, FUC, BMA, ZN, CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin chain a (EC 3.2.2.22) | protein | 258 | 40% helix, 22% strand | P02879 |
| B | Ricin chain B (EC 3.2.2.22) | protein | 261 | 13% helix, 37% strand | P02879 |
| C | Vhh antibody V11B2 | protein | 115 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 5 copies · chains A, B, C
- CL · Chloride ion · ion · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.82 | 0.93 | 44 | empty |
| 2 | 58 | 0.58 | 0.90 | 22 | CL |
| 3 | 218 | 0.52 | 0.77 | 32 | CL |
| 4 | 168 | 0.49 | 0.77 | 25 | empty |
| 5 | 131 | 0.49 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1613 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 809 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 210 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7KD2 · Ricin bound to VHH antibody V11B2 · 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 7KD2 · PDBe 7KD2 · UniProt P02879
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