MolNFT v1 · #180694 · protein
BG505 sosip MD39 in complex with the polyclonal Fab pabc-3 from animal RH.32034 (WK26 time point)
7L88 · BG505 sosip MD39 - GP120: “BG505 sosip MD39 in complex with the polyclonal Fab pabc-3 from animal RH.32034 (WK26 time point)”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.83). MolNFT v1 #180694 on…
- PDB
- 7L88
- Type
- protein
- Length
- 1,898 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 sosip MD39 - GP120; BG505 sosip MD39 - GP41; RH.32034 pabc-3 - heavy chain…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, C | BG505 sosip MD39 - GP120 | protein | 435 | 14% helix, 43% strand | — |
| F, B, E | BG505 sosip MD39 - GP41 | protein | 124 | 59% helix, 6% strand | — |
| H | RH.32034 pabc-3 - heavy chain | protein | 114 | 0% helix, 14% strand | — |
| L | RH.32034 pabc-3 - light chain | protein | 107 | 0% helix, 21% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 85 copies · chains D, C, F, A, B, L, E
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains D, A, C
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.83 | 0.93 | 43 | empty |
| 2 | 727 | 0.80 | 0.84 | 84 | empty |
| 3 | 673 | 0.78 | 0.83 | 73 | empty |
| 4 | 523 | 0.74 | 0.82 | 77 | empty |
| 5 | 358 | 0.73 | 0.85 | 58 | NAG |
Interfaces
18 interfaces between chains.
- C–E · 2344 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2319 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 2317 Ų buried · 17 hydrogen bonds · protein-protein
- F–B · 1027 Ų buried · 6 hydrogen bonds · protein-protein
- F–E · 1008 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 55 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L88 · BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26… · the same entry in another collection · chain D against D, 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 7L88 · PDBe 7L88
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