Research workbench
BG505 SOSIP.V5.2(7S) in complex with the polyclonal Fab pabc-1 from animal RH.33172 (WK38 time point)
Analyse BG505 SOSIP.V5.2(7S) in complex with the polyclonal Fab pabc-1 from animal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L8E
- Type
- protein
- Length
- 1,912 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; RH.33172 pabc-1 heavy chain; RH.33172 pabc-1 light chain
- UniProt
- Q2N0S5
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Envelope glycoprotein GP160 | protein | 444 | 16% helix, 40% strand | Q2N0S5 |
| D | Envelope glycoprotein GP160 | protein | 125 | 59% helix, 7% strand | Q2N0S5 |
| E | Envelope glycoprotein GP160 | protein | 441 | 16% helix, 41% strand | Q2N0S5 |
| F | Envelope glycoprotein GP160 | protein | 126 | 64% helix, 7% strand | Q2N0S5 |
| A | Envelope glycoprotein GP160 | protein | 445 | 15% helix, 40% strand | Q2N0S5 |
| B | Envelope glycoprotein GP160 | protein | 121 | 58% helix, 7% strand | Q2N0S5 |
| H | RH.33172 pabc-1 heavy chain | protein | 111 | 0% helix, 10% strand | — |
| L | RH.33172 pabc-1 light chain | protein | 99 | 5% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 86 copies · chains C, E, A, B, D, F, L
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A
- 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 | 716 | 0.82 | 0.86 | 87 | empty |
| 2 | 539 | 0.79 | 0.85 | 78 | NAG |
| 3 | 765 | 0.78 | 0.82 | 85 | empty |
| 4 | 489 | 0.77 | 0.85 | 62 | NAG |
| 5 | 559 | 0.77 | 0.84 | 87 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2364 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2348 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2316 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 967 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 944 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 65 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L8E · BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-1 from animal Rh.33172 (Wk38… · the same entry in another collection · chain C against C, 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 Q2N0S5
- Elsewhere: RCSB PDB 7L8E · PDBe 7L8E · UniProt Q2N0S5
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