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Crystal structure of the adcc-potent, weakly neutralizing HIV env co- receptor binding site antibody N12-I2 Fab in complex with HIV-1 clade A/E GP120 and M48U1
Analyse Crystal structure of the adcc-potent, weakly neutralizing HIV env co- receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W4M
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; Anti-HIV antibody N12-I2 Fab light chain; Anti-HIV…
- UniProt
- A0A0M3KKW9
- Ligands
- MPT, NAG, NH2
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 338 | 16% helix, 31% strand | A0A0M3KKW9 |
| L | Anti-HIV antibody N12-I2 Fab light chain | protein | 213 | 4% helix, 49% strand | — |
| H | Anti-HIV antibody N12-I2 Fab heavy chain | protein | 226 | 3% helix, 46% strand | — |
| N | M48U1 CD4 mimetic peptide | protein | 26 | 31% helix, 31% 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.64 | 0.93 | 19 | empty |
| 2 | 112 | 0.64 | 0.88 | 28 | empty |
| 3 | 380 | 0.62 | 0.78 | 48 | empty |
| 4 | 67 | 0.55 | 0.88 | 18 | NAG |
| 5 | 347 | 0.53 | 0.73 | 41 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1879 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1041 Ų buried · 14 hydrogen bonds · protein-protein
- G–N · 771 Ų buried · 5 hydrogen bonds · protein-protein
- G–L · 47 Ų buried · 1 hydrogen bond · protein-protein
- H–N · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 9 glycan, 3 modified, 2 covalent, 1 d-amino (disulfide, N-glycosylation, covalent ligand, sulfation, D-amino acid, nonstandard).
Compared structures
- 6W4M · Crystal structure of the adcc-potent, weakly neutralizing HIV env co-receptor binding… · 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
- Every structure of UniProt A0A0M3KKW9
- Elsewhere: RCSB PDB 6W4M · PDBe 6W4M · UniProt A0A0M3KKW9
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