MolNFT v1 · #159008 · protein
Ricin a chain bound to vhh antibody V8E6
6OBG: “Ricin a chain bound to vhh antibody V8E6”. X-ray diffraction, 2 ligands (ZN, CL), 8 pockets (best druggability 0.71). MolNFT v1 #159008 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OBG
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin a chain; Vhh antibody V8E6
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- ZN, CL
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ricin a chain (EC 3.2.2.22) | protein | 257 | 40% helix, 23% strand | P02879 |
| C | Vhh antibody V8E6 | protein | 116 | 5% helix, 53% strand | — |
| D | Vhh antibody V8E6 | protein | 116 | 5% helix, 53% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.98 | 18 | empty |
| 2 | 263 | 0.69 | 0.84 | 41 | empty |
| 3 | 294 | 0.68 | 0.83 | 46 | empty |
| 4 | 549 | 0.61 | 0.74 | 58 | empty |
| 5 | 122 | 0.44 | 0.77 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1239 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1210 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 425 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6OBG · Ricin A chain bound to VHH antibody V8E6 · 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 6OBG · PDBe 6OBG · UniProt P02879
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