Research workbench
BG505 sosip MD39 in complex with the polyclonal Fab pabc-4 from animal RH.32034 (WK26 time point)
Analyse BG505 sosip MD39 in complex with the polyclonal Fab pabc-4 from animal RH.32034… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L89
- Type
- protein
- Length
- 1,888 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RH.32034 pabc-4 - heavy chain; RH.32034 pabc-4 - light chain; BG505 sosip MD39 - GP120…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | RH.32034 pabc-4 - heavy chain | protein | 114 | 0% helix, 34% strand | — |
| L | RH.32034 pabc-4 - light chain | protein | 97 | 0% helix, 27% strand | — |
| E, A, B | BG505 sosip MD39 - GP120 | protein | 435 | 13% helix, 43% strand | — |
| F, C, D | BG505 sosip MD39 - GP41 | protein | 124 | 62% helix, 6% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 91 copies · chains E, B, F, A, C, D
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains E, A, B
- BMA · beta-D-mannopyranose · sugar · 3 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.83 | 0.92 | 42 | empty |
| 2 | 1089 | 0.77 | 0.79 | 103 | empty |
| 3 | 587 | 0.76 | 0.83 | 82 | empty |
| 4 | 397 | 0.71 | 0.82 | 62 | NAG |
| 5 | 505 | 0.70 | 0.81 | 72 | empty |
Interfaces
17 interfaces between chains.
- E–F · 2355 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 2272 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 2271 Ų buried · 17 hydrogen bonds · protein-protein
- F–D · 1028 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1011 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L89 · BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-4 from animal Rh.32034 (Wk26… · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 7L89 · PDBe 7L89
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