MolNFT v1 · #101463 · protein
Crystal structure of HIV-1 neutralizing antibody M66.6
4NRZ · M66.6 heavy chain: “Crystal structure of HIV-1 neutralizing antibody M66.6”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.70). MolNFT v1 #101463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4NRZ
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M66.6 heavy chain; M66.6 light chain
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | M66.6 heavy chain | protein | 226 | 10% helix, 56% strand | — |
| A | M66.6 heavy chain | protein | 225 | 8% helix, 54% strand | — |
| L | M66.6 light chain | protein | 213 | 6% helix, 50% strand | — |
| B | M66.6 light chain | protein | 212 | 6% helix, 49% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains H, A, L, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.70 | 0.77 | 68 | empty |
| 2 | 444 | 0.58 | 0.74 | 51 | empty |
| 3 | 228 | 0.45 | 0.73 | 28 | ZN |
| 4 | 226 | 0.44 | 0.73 | 32 | empty |
| 5 | 115 | 0.38 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1861 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1790 Ų buried · 12 hydrogen bonds · protein-protein
- L–B · 394 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4NRZ · Crystal Structure of HIV-1 Neutralizing Antibody m66.6 · the same entry in another collection · chain H against H, 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 4NRZ · PDBe 4NRZ
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