MolNFT v1 · #114423 · protein
Ricin a chain bound to camelid nanobody (VHH9)(E1)
5BOZ: “Ricin a chain bound to camelid nanobody (VHH9)(E1)”. X-ray diffraction, 2 ligands (SO4, CL), 20 pockets (best druggability 0.60). MolNFT v1 #114423 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BOZ
- Type
- protein
- Length
- 2,289 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin; Vhh single chain antibody E1
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Ricin (EC 3.2.2.22) | protein | 259 | 40% helix, 23% strand | P02879 |
| G, L | Vhh single chain antibody E1 | protein | 123 | 5% helix, 44% strand | — |
| B, F | Ricin (EC 3.2.2.22) | protein | 260 | 40% helix, 23% strand | P02879 |
| H, K | Vhh single chain antibody E1 | protein | 125 | 5% helix, 43% strand | — |
| I | Vhh single chain antibody E1 | protein | 118 | 5% helix, 44% strand | — |
| J | Vhh single chain antibody E1 | protein | 119 | 5% helix, 45% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 20 copies · chains A, G, B, H, C, D, I, J, E, K, F, L
- CL · Chloride ion · ion · 3 copies · chains D, E, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.60 | 0.79 | 46 | empty |
| 2 | 215 | 0.59 | 0.81 | 35 | empty |
| 3 | 220 | 0.56 | 0.78 | 34 | empty |
| 4 | 231 | 0.56 | 0.78 | 35 | empty |
| 5 | 228 | 0.55 | 0.78 | 34 | empty |
Interfaces
11 interfaces between chains.
- B–H · 1054 Ų buried · 20 hydrogen bonds · protein-protein
- E–K · 1054 Ų buried · 24 hydrogen bonds · protein-protein
- A–G · 1047 Ų buried · 21 hydrogen bonds · protein-protein
- F–L · 1018 Ų buried · 22 hydrogen bonds · protein-protein
- D–J · 872 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5BOZ · Ricin A chain bound to camelid nanobody (VHH9)(E1) · the same entry in another collection · chain B against B, 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 5BOZ · PDBe 5BOZ · UniProt P02879
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