MolNFT v1 · #114640 · protein
The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing il-1BETA
5BVP · Canakinumab Fab heavy-chain: “The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing…”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.64). MolNFT v1 #114640…
- PDB
- 5BVP
- Type
- protein
- Length
- 582 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Canakinumab Fab heavy-chain; Interleukin-1 beta; Canakinumab Fab light-chain
- UniProt
- P01584
- Ligands
- CL
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Canakinumab Fab heavy-chain | protein | 220 | 7% helix, 50% strand | — |
| I | Interleukin-1 beta | protein | 149 | 8% helix, 50% strand | P01584 |
| L | Canakinumab Fab light-chain | protein | 213 | 7% helix, 51% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.64 | 0.76 | 64 | empty |
| 2 | 283 | 0.56 | 0.77 | 37 | empty |
| 3 | 138 | 0.48 | 0.79 | 25 | empty |
| 4 | 76 | 0.33 | 0.75 | 12 | empty |
| 5 | 63 | 0.32 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1839 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 748 Ų buried · 16 hydrogen bonds · protein-protein
- I–L · 415 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5BVP · The molecular mode of action and species specificity of canakinumab, a human monoclonal… · the same entry in another collection · chain H against H, TM-score 1.00
- P01584 · AlphaFold monomer V2.0 prediction for interleukin-1 beta (P01584) · a predicted model of the same protein · chain I against A, TM-score 0.96
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 P01584
- Elsewhere: RCSB PDB 5BVP · PDBe 5BVP · UniProt P01584
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