Research workbench
Crystal structure of fully glycosylated HIV-1 GP120 core bound to CD4 and 17B Fab
Analyse Crystal structure of fully glycosylated HIV-1 GP120 core bound to CD4 and 17B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RQS
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-domain CD4; 17B Fab light chain; 17B Fab heavy chain; HIV-1 YU2 GP120 core chimeric…
- UniProt
- P01730, P35961
- Ligands
- NAG, MAN, BMA
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 2-domain CD4 | protein | 181 | 7% helix, 51% strand | P01730 |
| C | 17B Fab light chain | protein | 214 | 4% helix, 50% strand | — |
| D | 17B Fab heavy chain | protein | 223 | 4% helix, 52% strand | — |
| G | HIV-1 YU2 GP120 core chimeric protein | protein | 295 | 18% helix, 36% strand | P35961 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains G, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains G
- BMA · beta-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.73 | 0.98 | 20 | empty |
| 2 | 59 | 0.71 | 0.98 | 21 | empty |
| 3 | 305 | 0.62 | 0.80 | 28 | empty |
| 4 | 415 | 0.58 | 0.75 | 43 | empty |
| 5 | 77 | 0.51 | 0.84 | 21 | NAG |
Interfaces
4 interfaces between chains.
- C–D · 1798 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 1171 Ų buried · 16 hydrogen bonds · protein-protein
- D–G · 464 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 135 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4RQS · Crystal structure of fully glycosylated HIV-1 gp120 core bound to CD4 and 17b Fab · the same entry in another collection · chain B against B, TM-score 1.00
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P01730
- Every structure of UniProt P35961
- Elsewhere: RCSB PDB 4RQS · PDBe 4RQS · UniProt P01730 · UniProt P35961
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