Research workbench
CD4- and 17-bound HIV-1 env B41 sosip in complex with small molecule GO35
Analyse CD4- and 17-bound HIV-1 env B41 sosip in complex with small molecule GO35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OPN
- Type
- protein
- Length
- 1,713 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Envelope glycoprotein GP41; T-cell surface glycoprotein CD4
- UniProt
- B3UES2, B3UEZ6, P01730
- Ligands
- N07, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Envelope glycoprotein GP160 | protein | 352 | 17% helix, 37% strand | B3UES2 |
| B, E, H | Envelope glycoprotein GP41 | protein | 124 | 68% helix, 2% strand | B3UEZ6 |
| C, F, I | T-cell surface glycoprotein CD4 | protein | 95 | 9% helix, 43% strand | P01730 |
Ligands and binding sites
- N07 · [3'-(5-methyl-1,3,4-oxadiazol-2-yl)[1,1'-biphenyl]-3-yl](piperidin-1-yl)methanone · ligand · 3 copies · chains B, E, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, D, G
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, D, G
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.77 | 0.96 | 26 | empty |
| 2 | 115 | 0.77 | 0.96 | 26 | empty |
| 3 | 909 | 0.75 | 0.78 | 85 | N07 |
| 4 | 88 | 0.75 | 0.97 | 18 | empty |
| 5 | 816 | 0.74 | 0.78 | 71 | N07 |
Interfaces
15 interfaces between chains.
- D–E · 2160 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2155 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2152 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 932 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 929 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 glycan, 30 disulfide (N-glycosylation, disulfide).
Compared structures
- 6OPN · CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35 · the same entry in another collection · chain I against I, 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 I against A, TM-score 0.94
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 B3UES2
- Every structure of UniProt B3UEZ6
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 6OPN · PDBe 6OPN · UniProt B3UES2 · UniProt B3UEZ6 · UniProt P01730
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