MolNFT v1 · #124595 · protein
Crystal structure of the adcc-potent antibody N60-I3 Fab in complex with HIV-1 clade A/E GP120 W69A/S115W mutant and M48U1.
5KJR · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of the adcc-potent antibody N60-I3 Fab in complex with HIV-1 clade A/E GP120 W69A/S115W…”. X-ray diffraction, 3 ligands (MPT, NAG, NH2), 10 pockets (best druggability 0.64).…
- PDB
- 5KJR
- Type
- protein
- Length
- 788 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; M48U1 CD4 mimetic peptide; N60-I3 Fab heavy chain…
- UniProt
- A0A0M3KKW9
- Ligands
- MPT, NAG, NH2
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 332 | 14% helix, 32% strand | A0A0M3KKW9 |
| N | M48U1 CD4 mimetic peptide | protein | 26 | 35% helix, 31% strand | — |
| H | N60-I3 Fab heavy chain | protein | 218 | 3% helix, 46% strand | — |
| L | N60-I3 Fab light chain | protein | 212 | 7% helix, 44% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · chains N
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G
- NH2 · Amino group · ion · chains N
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 242 | 0.64 | 0.82 | 33 | empty |
| 2 | 122 | 0.61 | 0.86 | 25 | empty |
| 3 | 463 | 0.60 | 0.75 | 48 | empty |
| 4 | 113 | 0.55 | 0.83 | 30 | empty |
| 5 | 152 | 0.52 | 0.79 | 34 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1809 Ų buried · 12 hydrogen bonds · protein-protein
- G–N · 714 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 658 Ų buried · 11 hydrogen bonds · protein-protein
- G–L · 157 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 glycan, 2 covalent, 1 d-amino, 1 modified (disulfide, N-glycosylation, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 5KJR · 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
- Every structure of UniProt A0A0M3KKW9
- Elsewhere: RCSB PDB 5KJR · PDBe 5KJR · UniProt A0A0M3KKW9
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