Research workbench
Cryo-EM structure of CD4BS antibody AB1303 in complex with HIV-1 env trimer BG505 SOSIP.664
Analyse Cryo-EM structure of CD4BS antibody AB1303 in complex with HIV-1 env trimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TFN
- Type
- protein
- Length
- 2,344 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein BG505 SOSIP.664 - GP120; Anti-HIV-1 CD4BS antibody Fab AB1303…
- UniProt
- A0A6H1VH54, Q2N0S6
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 10 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein BG505 SOSIP.664 - GP120 | protein | 429 | 14% helix, 33% strand | A0A6H1VH54 |
| B | Envelope glycoprotein BG505 SOSIP.664 - GP120 | protein | 422 | 14% helix, 29% strand | A0A6H1VH54 |
| C | Envelope glycoprotein BG505 SOSIP.664 - GP120 | protein | 410 | 11% helix, 29% strand | A0A6H1VH54 |
| H, I, P | Anti-HIV-1 CD4BS antibody Fab AB1303 - heavy chain | protein | 123 | 5% helix, 50% strand | — |
| J | CD4 binding site antibody Fab AB1303 - light chain | protein | 111 | 5% helix, 48% strand | — |
| L | CD4 binding site antibody Fab AB1303 - light chain | protein | 112 | 3% helix, 46% strand | — |
| Q | CD4 binding site antibody Fab AB1303 - light chain | protein | 111 | 5% helix, 49% strand | — |
| X | Envelope glycoprotein BG505 SOSIP.664 - GP41 | protein | 132 | 62% helix, 2% strand | Q2N0S6 |
| Y | Envelope glycoprotein BG505 SOSIP.664 - GP41 | protein | 123 | 63% helix, 1% strand | Q2N0S6 |
| Z | Envelope glycoprotein BG505 SOSIP.664 - GP41 | protein | 125 | 63% helix, 7% strand | Q2N0S6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains A, L, B, J, C, Q, H
- BMA · beta-D-mannopyranose · sugar · 10 copies · chains L, A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.80 | 0.95 | 28 | empty |
| 2 | 1151 | 0.78 | 0.79 | 121 | empty |
| 3 | 1159 | 0.77 | 0.79 | 124 | empty |
| 4 | 148 | 0.74 | 0.92 | 35 | empty |
| 5 | 890 | 0.72 | 0.77 | 71 | empty |
Interfaces
22 interfaces between chains.
- A–X · 2485 Ų buried · 15 hydrogen bonds · protein-protein
- C–Z · 2334 Ų buried · 10 hydrogen bonds · protein-protein
- B–Y · 2325 Ų buried · 10 hydrogen bonds · protein-protein
- B–I · 1088 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1060 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 23 glycan (disulfide, N-glycosylation).
Compared structures
- 7TFN · Cryo-EM structure of CD4bs antibody Ab1303 in complex with HIV-1 Env trimer BG505… · 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 A0A6H1VH54
- Every structure of UniProt Q2N0S6
- Elsewhere: RCSB PDB 7TFN · PDBe 7TFN · UniProt A0A6H1VH54 · UniProt Q2N0S6
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