Research workbench
Crystal structure of broadly neutralizing antibody CR8043
Analyse Crystal structure of broadly neutralizing antibody CR8043 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NM4
- Type
- protein
- Length
- 880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody CR8043, light chain; Antibody CR8043, heavy chain
- UniProt
- P0DOX7, Q6N089
- Pockets
- 11 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Antibody CR8043, light chain | protein | 219 | 5% helix, 51% strand | P0DOX7 |
| H | Antibody CR8043, heavy chain | protein | 219 | 8% helix, 51% strand | Q6N089 |
| I | Antibody CR8043, heavy chain | protein | 223 | 8% helix, 51% strand | Q6N089 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains L, H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.58 | 0.76 | 49 | empty |
| 2 | 318 | 0.53 | 0.74 | 37 | PEG |
| 3 | 122 | 0.50 | 0.80 | 27 | empty |
| 4 | 56 | 0.44 | 0.84 | 23 | PEG |
| 5 | 103 | 0.41 | 0.77 | 27 | empty |
Interfaces
5 interfaces between chains.
- M–I · 2124 Ų buried · 19 hydrogen bonds · protein-protein
- L–H · 1915 Ų buried · 16 hydrogen bonds · protein-protein
- L–M · 311 Ų buried · 8 hydrogen bonds · protein-protein
- H–I · 55 Ų buried · 0 hydrogen bonds · protein-protein
- L–I · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4NM4 · Crystal structure of broadly neutralizing antibody CR8043 · the same entry in another collection · chain L against L, TM-score 1.00
- P0DOX7 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa light chain (P0DOX7) · a predicted model of the same protein · chain L against A, TM-score 0.95
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 P0DOX7
- Every structure of UniProt Q6N089
- Elsewhere: RCSB PDB 4NM4 · PDBe 4NM4 · UniProt P0DOX7 · UniProt Q6N089
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