MolNFT v1 · #180645 · protein
Cryo-EM structure of HIV-1 env CH848.3.D0949.10.17CHIM.6R.DS.SOSIP.664
7L6O · CH848.3.D0949.10.17CHIM.6R.DS.SOSIP.664 - GP120: “Cryo-EM structure of HIV-1 env CH848.3.D0949.10.17CHIM.6R.DS.SOSIP.664”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.83). MolNFT v1 #180645 on…
- PDB
- 7L6O
- Type
- protein
- Length
- 1,776 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH848.3.D0949.10.17CHIM.6R.DS.SOSIP.664 - GP120; CH848.3.D0949.10.17CHIM.6R.DS.SOSIP.664…
- UniProt
- A0A1W6IPB2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, c, e | CH848.3.D0949.10.17CHIM.6R.DS.SOSIP.664 - GP120 | protein | 466 | 14% helix, 36% strand | A0A1W6IPB2 |
| b, d, f | CH848.3.D0949.10.17CHIM.6R.DS.SOSIP.664 - GP41 | protein | 126 | 56% helix, 5% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 96 copies · chains a, e, c, b, d, f
- BMA · beta-D-mannopyranose · sugar · 30 copies · chains a, c
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains a, c, e
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.83 | 0.84 | 97 | empty |
| 2 | 58 | 0.64 | 0.94 | 16 | empty |
| 3 | 63 | 0.64 | 0.93 | 16 | empty |
| 4 | 675 | 0.64 | 0.74 | 56 | empty |
| 5 | 646 | 0.62 | 0.73 | 63 | empty |
Interfaces
12 interfaces between chains.
- c–d · 2560 Ų buried · 31 hydrogen bonds · protein-protein
- a–b · 2547 Ų buried · 29 hydrogen bonds · protein-protein
- e–f · 2540 Ų buried · 28 hydrogen bonds · protein-protein
- d–f · 1031 Ų buried · 10 hydrogen bonds · protein-protein
- b–f · 1020 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 36 disulfide (N-glycosylation, disulfide, O-glycosylation).
Compared structures
- 7L6O · Cryo-EM structure of HIV-1 Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 · the same entry in another collection · chain a against a, 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
- Every structure of UniProt A0A1W6IPB2
- Elsewhere: RCSB PDB 7L6O · PDBe 7L6O · UniProt A0A1W6IPB2
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