MolNFT v1 · #179712 · protein
Ricin bound to vhh antibody V5E4
7KDU · Ricin chain a: “Ricin bound to vhh antibody V5E4”. X-ray diffraction, 3 ligands (NAG, FUC, ZN), 6 pockets (best druggability 0.80). MolNFT v1 #179712 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KDU
- Type
- protein
- Length
- 611 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin chain a; Ricin chain B; Vhh antibody V5E4
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- NAG, FUC, ZN
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin chain a (EC 3.2.2.22) | protein | 256 | 39% helix, 21% strand | P02879 |
| B | Ricin chain B (EC 3.2.2.22) | protein | 257 | 9% helix, 38% strand | P02879 |
| C | Vhh antibody V5E4 | protein | 98 | 3% helix, 33% 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
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A, B
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 | 246 | 0.80 | 0.92 | 50 | EDO |
| 2 | 173 | 0.63 | 0.85 | 36 | empty |
| 3 | 272 | 0.54 | 0.76 | 37 | empty |
| 4 | 122 | 0.41 | 0.76 | 23 | empty |
| 5 | 124 | 0.40 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1626 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KDU · Ricin bound to VHH antibody V5E4 · 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 7KDU · PDBe 7KDU · UniProt P02879
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