Research workbench
Cryo-et subtomogram averaging of BG505 SOSIP.664 in complex with SCD4, 17B, and 8ANC195
Analyse Cryo-et subtomogram averaging of BG505 SOSIP.664 in complex with SCD4, 17B, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A8H
- Type
- protein
- Length
- 4,104 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 GP120; T-cell surface glycoprotein CD4; Fab of broadly neutralizing antibody 17B…
- UniProt
- P01730
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 6 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, M | HIV-1 GP120 | protein | 306 | 15% helix, 37% strand | — |
| B, H, N | T-cell surface glycoprotein CD4 | protein | 181 | 6% helix, 41% strand | P01730 |
| C, I, O | Fab of broadly neutralizing antibody 17B | protein | 214 | 4% helix, 46% strand | — |
| D, J, P | Fab of broadly neutralizing antibody 17B | protein | 229 | 8% helix, 48% strand | — |
| E, K, Q | Fab of broadly neutralizing antibody 8ANC195 variant G52K5 | protein | 214 | 7% helix, 50% strand | — |
| F, L, R | Fab of broadly neutralizing antibody 8ANC195 variant G52K5 | protein | 224 | 8% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, F, G, L, M, Q, R
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 | 64 | 0.73 | 0.99 | 24 | empty |
| 2 | 67 | 0.72 | 0.98 | 25 | empty |
| 3 | 64 | 0.72 | 0.98 | 25 | empty |
| 4 | 701 | 0.70 | 0.77 | 83 | NAG |
| 5 | 468 | 0.65 | 0.78 | 47 | empty |
Interfaces
25 interfaces between chains.
- O–P · 1896 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1890 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1888 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1780 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1771 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 glycan, 51 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5A8H · cryo-ET subtomogram averaging of BG505 SOSIP.664 in complex with sCD4, 17b, and 8ANC195 · the same entry in another collection · chain R against R, 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 P01730
- Elsewhere: RCSB PDB 5A8H · PDBe 5A8H · UniProt P01730
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