MolNFT v1 · #145721 · protein
Ricin catalytic subunit bound go A9 vhh antibody
6CWG: “Ricin catalytic subunit bound go A9 vhh antibody”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.74). MolNFT v1 #145721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CWG
- Type
- protein
- Length
- 775 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin; Vhh antibody
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin (EC 3.2.2.22) | protein | 262 | 38% helix, 23% strand | P02879 |
| B, D | Vhh antibody | protein | 127 | 11% helix, 49% strand | — |
| C | Ricin (EC 3.2.2.22) | protein | 259 | 38% helix, 23% strand | P02879 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.74 | 0.77 | 84 | empty |
| 2 | 259 | 0.57 | 0.78 | 34 | empty |
| 3 | 73 | 0.38 | 0.77 | 17 | empty |
| 4 | 56 | 0.37 | 0.78 | 11 | empty |
| 5 | 70 | 0.37 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 609 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 602 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 178 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6CWG · Ricin catalytic subunit bound go A9 VHH antibody · 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 6CWG · PDBe 6CWG · UniProt P02879
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