Research workbench
Crystal structure of mouse anti-HIV potent neutralizing antibody M4H2K1
Analyse Crystal structure of mouse anti-HIV potent neutralizing antibody M4H2K1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KKZ
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab fragment of mouse monoclonal antibody M4H2K1; Heavy chain of Fab…
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of Fab fragment of mouse monoclonal antibody M4H2K1 | protein | 218 | 6% helix, 51% strand | — |
| H | Heavy chain of Fab fragment of mouse monoclonal antibody M4H2K1 | protein | 222 | 9% helix, 49% strand | — |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains L, H
- EDO · 1,2-ethanediol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.63 | 0.80 | 45 | empty |
| 2 | 198 | 0.51 | 0.77 | 31 | empty |
| 3 | 59 | 0.50 | 0.87 | 23 | empty |
| 4 | 92 | 0.36 | 0.75 | 16 | empty |
| 5 | 68 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 1958 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7KKZ · Crystal structure of mouse anti-HIV potent neutralizing antibody M4H2K1 · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 7KKZ · PDBe 7KKZ
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