Research workbench
Structure of HIV-1 GP120 with GP41-interactive region: layered architecture and basis of conformational mobility
Analyse Structure of HIV-1 GP120 with GP41-interactive region: layered architecture and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JWO
- Type
- protein
- Length
- 966 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 GP120 envelope glycoprotein; T-cell surface glycoprotein CD4; Fab 48D light chain…
- UniProt
- P01730
- Ligands
- NAG, FUL
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 GP120 envelope glycoprotein | protein | 353 | 15% helix, 35% strand | — |
| C | T-cell surface glycoprotein CD4 | protein | 184 | 5% helix, 49% strand | P01730 |
| L | Fab 48D light chain | protein | 209 | 1% helix, 47% strand | — |
| H | Fab 48D heavy chain | protein | 220 | 4% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C
- FUL · beta-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.70 | 0.99 | 21 | empty |
| 2 | 507 | 0.61 | 0.75 | 57 | empty |
| 3 | 242 | 0.60 | 0.80 | 33 | empty |
| 4 | 328 | 0.59 | 0.78 | 38 | empty |
| 5 | 109 | 0.55 | 0.83 | 26 | NAG |
Interfaces
4 interfaces between chains.
- L–H · 1757 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 994 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 467 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 383 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 3JWO · Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of… · the same entry in another collection · chain C against C, 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 C against A, TM-score 0.91
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
- Elsewhere: RCSB PDB 3JWO · PDBe 3JWO · UniProt P01730
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