Research workbench
BG505-sosip model reconstructed by subparticle extraction and refinement from a tetrahedral nanoparticle T33_DN10
Analyse BG505-sosip model reconstructed by subparticle extraction and refinement from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VFL
- Type
- protein
- Length
- 1,710 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505-SOSIPV5.2(7S) - GP120; BG505-SOSIPV5.2(7S) - GP41
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | BG505-SOSIPV5.2(7S) - GP120 | protein | 448 | 16% helix, 41% strand | — |
| B, D, F | BG505-SOSIPV5.2(7S) - GP41 | protein | 122 | 62% helix, 7% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, E, B, C, D, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, C, E
- 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 | 308 | 0.83 | 0.93 | 48 | empty |
| 2 | 346 | 0.71 | 0.83 | 48 | NAG |
| 3 | 360 | 0.69 | 0.82 | 53 | NAG |
| 4 | 418 | 0.69 | 0.81 | 64 | NAG |
| 5 | 809 | 0.68 | 0.75 | 72 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2538 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2528 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2528 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1155 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1153 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 6VFL · BG505-SOSIP model reconstructed by subparticle extraction and refinement from a… · the same entry in another collection · chain A against A, 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 6VFL · PDBe 6VFL
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