MolNFT v1 · #134402 · protein
Crystal structure of strain-specific glycan-dependent CD4 binding site-directed neutralizing antibody CAP257-RH1, in complex with HIV-1 strain rhpa GP120 core with an oligomannose N276 glycan.
5T33 · CAP257-RH1 heavy chain: “Crystal structure of strain-specific glycan-dependent CD4 binding site-directed neutralizing antibody…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 9 pockets (best druggability 0.72). MolNFT v1 #134402 on…
- PDB
- 5T33
- Type
- protein
- Length
- 754 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAP257-RH1 heavy chain; CAP257-RH1 light chain; Rhpa GP120 core
- Ligands
- NAG, MAN, BMA
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CAP257-RH1 heavy chain | protein | 223 | 4% helix, 50% strand | — |
| L | CAP257-RH1 light chain | protein | 212 | 8% helix, 48% strand | — |
| G | Rhpa GP120 core | protein | 319 | 17% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains G, H, L
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains H, L
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains G, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.72 | 0.76 | 89 | empty |
| 2 | 369 | 0.67 | 0.81 | 51 | empty |
| 3 | 76 | 0.57 | 0.87 | 16 | NAG |
| 4 | 190 | 0.51 | 0.78 | 23 | empty |
| 5 | 104 | 0.50 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2067 Ų buried · 16 hydrogen bonds · protein-protein
- H–G · 420 Ų buried · 6 hydrogen bonds · protein-protein
- L–G · 298 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5T33 · Crystal structure of strain-specific glycan-dependent CD4 binding site-directed… · the same entry in another collection · chain H against H, 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 5T33 · PDBe 5T33
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