Research workbench
Cryo-EM structure of T/F100 SOSIP.664 HIV-1 env trimer in complex with 8ANC195 Fab
Analyse Cryo-EM structure of T/F100 SOSIP.664 HIV-1 env trimer in complex with 8ANC195… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NQD
- Type
- protein
- Length
- 2,403 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T/F100 env GP120; T/F100 env GP41; 8ANC195 G52K5 heavy chain, ig gamma-1 chain; 8ANC195…
- UniProt
- A0A140EMT3, S6B2A6, P0DOX7
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 4 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | T/F100 env GP120 | protein | 439 | 10% helix, 35% strand | A0A140EMT3 |
| B, F, J | T/F100 env GP41 | protein | 124 | 57% helix, 5% strand | A0A140EMT3 |
| C, G, K | 8ANC195 G52K5 heavy chain, ig gamma-1 chain | protein | 130 | 0% helix, 45% strand | S6B2A6 |
| D, H, L | 8ANC195 G52K5 light chain | protein | 108 | 3% helix, 46% strand | P0DOX7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 96 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
- MAN · alpha-D-mannopyranose · sugar · 33 copies · chains C, D, G, H, K, L
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains C, D, G, H, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.77 | 0.79 | 149 | empty |
| 2 | 106 | 0.71 | 0.93 | 24 | empty |
| 3 | 688 | 0.68 | 0.76 | 78 | empty |
| 4 | 299 | 0.64 | 0.80 | 56 | empty |
| 5 | 332 | 0.63 | 0.79 | 51 | empty |
Interfaces
24 interfaces between chains.
- A–B · 2234 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 2234 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 2232 Ų buried · 8 hydrogen bonds · protein-protein
- F–J · 1061 Ų buried · 7 hydrogen bonds · protein-protein
- B–J · 1049 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NQD · Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab · the same entry in another collection · chain L against L, 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 A0A140EMT3
- Every structure of UniProt S6B2A6
- Every structure of UniProt P0DOX7
- Elsewhere: RCSB PDB 6NQD · PDBe 6NQD · UniProt A0A140EMT3 · UniProt S6B2A6 · UniProt P0DOX7
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