MolNFT v1 · #105789 · protein
Crystal structure of the adcc-potent antibody N60-I3 Fab in complex with HIV-1 clade A/E GP120 and M48U1
4RFO: “Crystal structure of the adcc-potent antibody N60-I3 Fab in complex with HIV-1 clade A/E GP120 and M48U1”. X-ray diffraction, 3 ligands (MPT, NAG, NH2), 12 pockets (best druggability 0.62). MolNFT v1 #105789 on GenesisL1: 3D…
- PDB
- 4RFO
- Type
- protein
- Length
- 788 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 clade A/E GP120; M48U1 CD4 mimetic peptide; N60-I3 Fab heavy chain; N60-I3 Fab…
- Ligands
- MPT, NAG, NH2
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | HIV-1 clade A/E GP120 | protein | 336 | 17% helix, 30% strand | — |
| N | M48U1 CD4 mimetic peptide | protein | 26 | 35% helix, 23% strand | — |
| H | N60-I3 Fab heavy chain | protein | 214 | 3% helix, 44% strand | — |
| L | N60-I3 Fab light chain | protein | 212 | 6% helix, 44% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · chains G, N
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains G
- NH2 · Amino group · ion · chains N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.62 | 0.89 | 21 | NAG |
| 2 | 132 | 0.60 | 0.85 | 28 | empty |
| 3 | 477 | 0.60 | 0.74 | 53 | empty |
| 4 | 66 | 0.58 | 0.89 | 18 | empty |
| 5 | 130 | 0.47 | 0.78 | 28 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1751 Ų buried · 11 hydrogen bonds · protein-protein
- G–N · 740 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 644 Ų buried · 8 hydrogen bonds · protein-protein
- G–L · 137 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide, 9 glycan, 2 covalent, 1 d-amino, 1 modified (disulfide, N-glycosylation, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 4RFO · Crystal structure of the ADCC-Potent Antibody N60-I3 Fab in complex with HIV-1 Clade A/E… · the same entry in another collection · chain G against G, 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 4RFO · PDBe 4RFO
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