Research workbench
BG505 sosip MD39 in complex with the polyclonal Fab pabc-1 from animal RH.33104 (WK26 time point)
Analyse BG505 sosip MD39 in complex with the polyclonal Fab pabc-1 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
- 7L8A
- Type
- protein
- Length
- 1,907 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-1 - heavy chain…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | BG505 sosip MD39 - GP120 | protein | 440 | 13% helix, 43% strand | — |
| F | BG505 sosip MD39 - GP41 | protein | 120 | 58% helix, 8% strand | — |
| H | RH.33104 pabc-1 - heavy chain | protein | 115 | 5% helix, 48% strand | — |
| L | RH.33104 pabc-1 - light chain | protein | 105 | 0% helix, 44% strand | — |
| A | BG505 sosip MD39 - GP120 | protein | 443 | 12% helix, 44% strand | — |
| B | BG505 sosip MD39 - GP41 | protein | 122 | 61% helix, 6% strand | — |
| C | BG505 sosip MD39 - GP120 | protein | 439 | 14% helix, 45% strand | — |
| D | BG505 sosip MD39 - GP41 | protein | 123 | 65% helix, 7% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 89 copies · chains E, C, F, A, D, L, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains E, 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 | 365 | 0.84 | 0.92 | 46 | empty |
| 2 | 862 | 0.83 | 0.86 | 125 | empty |
| 3 | 509 | 0.77 | 0.85 | 66 | empty |
| 4 | 497 | 0.73 | 0.83 | 61 | empty |
| 5 | 77 | 0.70 | 0.95 | 26 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2470 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2398 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2250 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 996 Ų buried · 9 hydrogen bonds · protein-protein
- F–B · 955 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L8A · BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-1 from animal Rh.33104 (Wk26… · the same entry in another collection · chain B against B, 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 7L8A · PDBe 7L8A
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