Research workbench
Ricin a chain bound to vhh antibody V6D4
Analyse Ricin a chain bound to vhh antibody V6D4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OCD
- Type
- protein
- Length
- 750 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin a chain; Vhh antibody V6D4
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- ZN, CL
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin a chain (EC 3.2.2.22) | protein | 257 | 41% helix, 23% strand | P02879 |
| B | Vhh antibody V6D4 | protein | 114 | 8% helix, 42% strand | — |
| C | Ricin a chain (EC 3.2.2.22) | protein | 258 | 41% helix, 23% strand | P02879 |
| D | Vhh antibody V6D4 | protein | 121 | 5% helix, 44% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, C
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, D
- IMD · Imidazole · additive · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.80 | 0.84 | 98 | EDO |
| 2 | 535 | 0.75 | 0.83 | 71 | EDO |
| 3 | 72 | 0.70 | 0.96 | 20 | empty |
| 4 | 123 | 0.61 | 0.86 | 18 | empty |
| 5 | 63 | 0.40 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1009 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 979 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 57 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6OCD · Ricin A chain bound to VHH antibody V6D4 · 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 6OCD · PDBe 6OCD · UniProt P02879
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.