Research workbench
BG505.MD39TS env trimer in complex with Fab from antibody C05
Analyse BG505.MD39TS env trimer in complex with Fab from antibody C05 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SQ1
- Type
- protein
- Length
- 2,157 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein GP41; Envelope glycoprotein GP160; C05 Fab light chain; C05 Fab…
- UniProt
- Q2N0S6
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F | Transmembrane protein GP41 | protein | 121 | 69% helix, 6% strand | Q2N0S6 |
| C | Envelope glycoprotein GP160 | protein | 440 | 13% helix, 40% strand | Q2N0S6 |
| E | Envelope glycoprotein GP160 | protein | 446 | 13% helix, 40% strand | Q2N0S6 |
| L, I | C05 Fab light chain | protein | 111 | 3% helix, 49% strand | — |
| H, A | C05 Fab heavy chain | protein | 121 | 7% helix, 50% strand | — |
| G | Envelope glycoprotein GP160 | protein | 444 | 13% helix, 40% strand | Q2N0S6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 91 copies · chains C, E, H, G, A, B, D, F
- BMA · beta-D-mannopyranose · sugar · 5 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
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 | 1036 | 0.83 | 0.84 | 94 | empty |
| 2 | 69 | 0.71 | 0.96 | 18 | empty |
| 3 | 66 | 0.70 | 0.96 | 24 | empty |
| 4 | 103 | 0.69 | 0.92 | 21 | empty |
| 5 | 259 | 0.69 | 0.84 | 51 | NAG |
Interfaces
18 interfaces between chains.
- D–E · 2388 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 2337 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2327 Ų buried · 12 hydrogen bonds · protein-protein
- I–A · 915 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 892 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 37 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SQ1 · BG505.MD39TS Env trimer in complex with Fab from antibody C05 · the same entry in another collection · chain I against I, 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 Q2N0S6
- Elsewhere: RCSB PDB 7SQ1 · PDBe 7SQ1 · UniProt Q2N0S6
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