Research workbench
Ricin bound to vhh antibody V5E1
Analyse Ricin bound to vhh antibody V5E1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KBI
- Type
- protein
- Length
- 641 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin chain a; Ricin chain B; Vhh antibody V5E1
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- NAG, BMA, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin chain a (EC 3.2.2.22) | protein | 259 | 39% helix, 23% strand | P02879 |
| B | Ricin chain B (EC 3.2.2.22) | protein | 256 | 8% helix, 36% strand | P02879 |
| C | Vhh antibody V5E1 | protein | 126 | 7% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- CL · Chloride ion · ion · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.81 | 0.93 | 50 | empty |
| 2 | 387 | 0.61 | 0.77 | 36 | empty |
| 3 | 200 | 0.59 | 0.81 | 35 | empty |
| 4 | 262 | 0.57 | 0.78 | 35 | empty |
| 5 | 98 | 0.50 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1671 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 590 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 235 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7KBI · Ricin bound to VHH antibody V5E1 · 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 7KBI · PDBe 7KBI · UniProt P02879
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