Research workbench
Crystal structure of the non-neutralizing and adcc-potent C11-like antibody N12-I3 in complex with HIV-1 clade A/E GP120, the CD4 mimetic M48U1, and the antibody N5-I5.
Analyse Crystal structure of the non-neutralizing and adcc-potent C11-like antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W4L
- Type
- protein
- Length
- 2,460 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; CD4 mimetic peptide M48U1; Antibody N5-I5 Fab heavy…
- UniProt
- A0A0M3KKW9
- Ligands
- MPT, NAG, NH2, CL
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 357 | 17% helix, 38% strand | A0A0M3KKW9 |
| N, M | CD4 mimetic peptide M48U1 | protein | 26 | 35% helix, 23% strand | — |
| H, F | Antibody N5-I5 Fab heavy chain | protein | 212 | 3% helix, 45% strand | — |
| L, I | Antibody N5-I5 light chain | protein | 212 | 8% helix, 44% strand | — |
| D, B | Antibody N12-I3 Fab heavy chain | protein | 211 | 6% helix, 51% strand | — |
| E | Antibody N12-I3 light chain | protein | 213 | 6% helix, 46% strand | — |
| A | Clade A/E 93TH057 HIV-1 GP120 core | protein | 356 | 16% helix, 37% strand | A0A0M3KKW9 |
| C | Antibody N12-I3 light chain | protein | 212 | 4% helix, 46% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · 2 copies · chains G, N, A, M
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains G, E, A
- NH2 · Amino group · ion · 2 copies · chains N, M
- CL · Chloride ion · ion · 2 copies · chains G, N, A, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.73 | 0.80 | 87 | empty |
| 2 | 465 | 0.72 | 0.82 | 64 | empty |
| 3 | 784 | 0.70 | 0.77 | 101 | empty |
| 4 | 146 | 0.61 | 0.85 | 28 | empty |
| 5 | 414 | 0.59 | 0.75 | 56 | empty |
Interfaces
20 interfaces between chains.
- D–E · 1766 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1742 Ų buried · 16 hydrogen bonds · protein-protein
- F–I · 1672 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1635 Ų buried · 16 hydrogen bonds · protein-protein
- G–D · 756 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 21 glycan, 4 covalent, 2 d-amino, 2 modified (disulfide, N-glycosylation, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 5W4L · Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in… · 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 5W4L · PDBe 5W4L · UniProt A0A0M3KKW9
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