Research workbench
Crystal structure of HIV-1 neutralizing antibody M66
Analyse Crystal structure of HIV-1 neutralizing antibody M66 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NRY
- Type
- protein
- Length
- 844 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M66 heavy chain; M66 light chain
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | M66 heavy chain | protein | 207 | 5% helix, 51% strand | — |
| B | M66 heavy chain | protein | 205 | 6% helix, 52% strand | — |
| H | M66 light chain | protein | 214 | 7% helix, 54% strand | — |
| A | M66 light chain | protein | 218 | 7% helix, 55% strand | — |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.68 | 0.84 | 36 | empty |
| 2 | 415 | 0.64 | 0.78 | 45 | empty |
| 3 | 624 | 0.63 | 0.74 | 54 | empty |
| 4 | 573 | 0.60 | 0.74 | 56 | empty |
| 5 | 297 | 0.60 | 0.79 | 30 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1897 Ų buried · 16 hydrogen bonds · protein-protein
- B–A · 1819 Ų buried · 11 hydrogen bonds · protein-protein
- H–A · 443 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 253 Ų buried · 2 hydrogen bonds · protein-protein
- L–A · 246 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4NRY · Crystal Structure of HIV-1 Neutralizing Antibody m66 · 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 4NRY · PDBe 4NRY
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