Research workbench
Negative stain EM of BG505 SOSIP.664 in complex with SCD4, 17B, and 8ANC195
Analyse Negative stain EM of BG505 SOSIP.664 in complex with SCD4, 17B, and 8ANC195 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A7X
- Type
- protein
- Length
- 4,104 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 YU2 GP120; T-cell surface glycoprotein CD4; Fab of broadly neutralizing antibody…
- UniProt
- P01730
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 6 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | HIV-1 YU2 GP120 | protein | 306 | 15% helix, 38% strand | — |
| B, F, J | T-cell surface glycoprotein CD4 | protein | 181 | 6% helix, 41% strand | P01730 |
| C, G, K | Fab of broadly neutralizing antibody 17B | protein | 214 | 4% helix, 46% strand | — |
| D, H, L | Fab of broadly neutralizing antibody 17B | protein | 229 | 8% helix, 48% strand | — |
| M, O, Q | Fab of broadly neutralizing antibody 8ANC195 | protein | 214 | 7% helix, 50% strand | — |
| N, P, R | Fab of broadly neutralizing antibody 8ANC195 | protein | 224 | 8% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, N, E, P, I, 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 | 56 | 0.72 | 0.99 | 23 | empty |
| 2 | 59 | 0.71 | 0.98 | 23 | empty |
| 3 | 59 | 0.70 | 0.98 | 24 | empty |
| 4 | 555 | 0.63 | 0.75 | 64 | empty |
| 5 | 454 | 0.61 | 0.76 | 54 | empty |
Interfaces
18 interfaces between chains.
- C–D · 1901 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1890 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1889 Ų buried · 12 hydrogen bonds · protein-protein
- O–P · 1773 Ų buried · 16 hydrogen bonds · protein-protein
- Q–R · 1769 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 45 glycan (disulfide, N-glycosylation).
Compared structures
- 5A7X · negative stain EM 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 5A7X · PDBe 5A7X · UniProt P01730
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