Research workbench
Crystal structure of non-neutralizing, A32-like antibody 2.2C in complex with HIV-1 YU2 GP120
Analyse Crystal structure of non-neutralizing, A32-like antibody 2.2C in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R4F
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 env GP120; Antibody 2.2C light chain; Antibody 2.2C heavy chain; M48U1 peptide
- Ligands
- MPT, NAG, SO4, NH2
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 env GP120 | protein | 340 | 17% helix, 36% strand | — |
| L | Antibody 2.2C light chain | protein | 209 | 5% helix, 51% strand | — |
| H | Antibody 2.2C heavy chain | protein | 219 | 8% helix, 51% strand | — |
| R | M48U1 peptide | protein | 26 | 42% helix, 31% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · chains A, R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, H
- SO4 · Sulfate ion · ion · 2 copies · chains L, H
- NH2 · Amino group · ion · chains A, R
- BU3 · (R,R)-2,3-butanediol · additive · 3 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.60 | 0.83 | 29 | empty |
| 2 | 353 | 0.57 | 0.75 | 45 | empty |
| 3 | 55 | 0.50 | 0.87 | 19 | empty |
| 4 | 63 | 0.48 | 0.84 | 17 | NAG |
| 5 | 77 | 0.45 | 0.82 | 23 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1860 Ų buried · 16 hydrogen bonds · protein-protein
- A–R · 731 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 697 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 340 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide, 8 glycan, 2 covalent, 2 modified, 1 d-amino (disulfide, N-glycosylation, covalent ligand, nonstandard, D-amino acid).
Compared structures
- 4R4F · Crystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 YU2… · the same entry in another collection · chain A against A, 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 4R4F · PDBe 4R4F
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