Research workbench
Structural basis of coreceptor recognition by HIV-1 envelope spike
Analyse Structural basis of coreceptor recognition by HIV-1 envelope spike in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MET
- Type
- protein
- Length
- 1,074 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.5
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- Envelope glycoprotein gp160; T-cell surface glycoprotein CD4; C-C chemokine receptor type…
- UniProt
- Q70145, P01730, P51681
- Ligands
- NAG, BMA, MAN, A2G
- Pockets
- 18 · best druggability 0.76
Structure
electron microscopy · resolution 4.5 · 3 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein gp160 | protein | 398 | 14% helix, 28% strand | Q70145 |
| A | T-cell surface glycoprotein CD4 | protein | 363 | 3% helix, 40% strand | P01730 |
| B | C-C chemokine receptor type 5 | protein | 313 | 70% helix, 1% strand | P51681 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains G
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains G
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains G, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.76 | 0.80 | 84 | empty |
| 2 | 77 | 0.75 | 0.98 | 20 | empty |
| 3 | 76 | 0.72 | 0.97 | 26 | empty |
| 4 | 472 | 0.70 | 0.81 | 58 | empty |
| 5 | 331 | 0.64 | 0.80 | 48 | empty |
Interfaces
3 interfaces between chains.
- G–B · 2064 Ų buried · 32 hydrogen bonds · protein-protein
- G–A · 1378 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 12 disulfide, 2 modified (N-glycosylation, disulfide, sulfation, O-glycosylation).
Compared structures
- 6MET · Structural basis of coreceptor recognition by HIV-1 envelope spike · the same entry in another collection · chain A against A, TM-score 1.00
- P51681 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 5 (P51681) · a predicted model of the same protein · chain B against A, TM-score 0.92
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q70145
- Every structure of UniProt P01730
- Every structure of UniProt P51681
- Elsewhere: RCSB PDB 6MET · PDBe 6MET · UniProt Q70145 · UniProt P01730 · UniProt P51681
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