Research workbench
Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122
Analyse Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NF2
- Type
- protein
- Length
- 3,867 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- Envelope glycoprotein gp120; Envelope glycoprotein gp41; VRC03 Heavy Chain; VRC03 Light…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · resolution 3.7 · 8 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, Q | Envelope glycoprotein gp120 | protein | 453 | 10% helix, 38% strand | Q2N0S6 |
| B, I, R | Envelope glycoprotein gp41 | protein | 132 | 54% helix, 10% strand | Q2N0S6 |
| C, N, V | VRC03 Heavy Chain | protein | 128 | 5% helix, 47% strand | — |
| D, M, U | VRC03 Light Chain | protein | 102 | 0% helix, 46% strand | — |
| E, J, S | PGT122 Heavy Chain | protein | 132 | 2% helix, 44% strand | — |
| F, K, T | PGT122 Light Chain | protein | 105 | 3% helix, 38% strand | — |
| H, O, W | 0PV-c.01 Heavy Chain | protein | 125 | 5% helix, 55% strand | — |
| L, P, X | 0PV-c.01 Light Chain | protein | 112 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 105 copies · chains A, J, K, N, M, B, G, E, F, C, D, Q, S, T, V, U, I, R
- MAN · alpha-D-mannopyranose · sugar · 48 copies · chains J, K, N, A, M, E, F, C, G, D, S, T, V, Q, U
- BMA · beta-D-mannopyranose · sugar · 33 copies · chains J, A, N, E, G, C, S, Q, V
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 | 238 | 0.80 | 0.93 | 41 | empty |
| 2 | 1106 | 0.76 | 0.78 | 102 | NAG |
| 3 | 778 | 0.75 | 0.80 | 70 | NAG |
| 4 | 770 | 0.75 | 0.80 | 73 | NAG |
| 5 | 456 | 0.75 | 0.84 | 48 | NAG |
Interfaces
48 interfaces between chains.
- B–G · 2484 Ų buried · 20 hydrogen bonds · protein-protein
- A–I · 2483 Ų buried · 19 hydrogen bonds · protein-protein
- Q–R · 2479 Ų buried · 19 hydrogen bonds · protein-protein
- A–N · 1214 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 1211 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 51 disulfide (N-glycosylation, disulfide).
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 Q2N0S6
- Elsewhere: RCSB PDB 6NF2 · PDBe 6NF2 · UniProt Q2N0S6
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