Research workbench
BG505 sosip MD39 in complex with the polyclonal Fab pabc-3 from animal RH.33104 (WK26 time point)
Analyse BG505 sosip MD39 in complex with the polyclonal Fab pabc-3 from animal RH.33104… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L8C
- Type
- protein
- Length
- 1,911 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 sosip MD39 - GP120; BG505 sosip MD39 - GP41; RH.33104 pabc-3 - heavy chain…
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | BG505 sosip MD39 - GP120 | protein | 439 | 14% helix, 43% strand | — |
| B | BG505 sosip MD39 - GP41 | protein | 124 | 61% helix, 6% strand | — |
| E, F | BG505 sosip MD39 - GP41 | protein | 125 | 61% helix, 7% strand | — |
| H | RH.33104 pabc-3 - heavy chain | protein | 113 | 5% helix, 39% strand | — |
| L | RH.33104 pabc-3 - light chain | protein | 107 | 0% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 101 copies · chains A, D, B, C, E, L, F
- BMA · beta-D-mannopyranose · sugar · 6 copies
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains D
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 | 368 | 0.83 | 0.92 | 44 | empty |
| 2 | 915 | 0.79 | 0.81 | 85 | empty |
| 3 | 583 | 0.77 | 0.84 | 79 | empty |
| 4 | 665 | 0.75 | 0.81 | 80 | empty |
| 5 | 381 | 0.72 | 0.83 | 57 | NAG |
Interfaces
18 interfaces between chains.
- D–F · 2365 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 2319 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2273 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 971 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 958 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 59 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L8C · BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (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 7L8C · PDBe 7L8C
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