Research workbench
Ricin a chain bound to vhh antibody V2G10
Analyse Ricin a chain bound to vhh antibody V2G10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OCA
- Type
- protein
- Length
- 784 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin a chain; Vhh antibody V2G10
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- CL
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin a chain (EC 3.2.2.22) | protein | 256 | 41% helix, 23% strand | P02879 |
| C | Vhh antibody V2G10 | protein | 125 | 10% helix, 45% strand | — |
| B | Ricin a chain (EC 3.2.2.22) | protein | 265 | 39% helix, 22% strand | P02879 |
| D | Vhh antibody V2G10 | protein | 138 | 13% helix, 46% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.78 | 0.85 | 49 | empty |
| 2 | 628 | 0.77 | 0.83 | 58 | empty |
| 3 | 88 | 0.74 | 0.97 | 25 | empty |
| 4 | 122 | 0.70 | 0.92 | 33 | empty |
| 5 | 355 | 0.56 | 0.75 | 40 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1082 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1013 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 350 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6OCA · Ricin A chain bound to VHH antibody V2G10 · 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 6OCA · PDBe 6OCA · UniProt P02879
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