Research workbench
Glutaraldehyde-treated BG505 SOSIP.664 env in complex with PGV04 Fab
Analyse Glutaraldehyde-treated BG505 SOSIP.664 env in complex with PGV04 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CRQ
- Type
- protein
- Length
- 2,391 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; PGV04 vh; PGV04 vl
- UniProt
- Q2N0S5, Q2N0S7
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Envelope glycoprotein GP160 | protein | 450 | 15% helix, 36% strand | Q2N0S5 |
| C, G, H | Envelope glycoprotein GP160 | protein | 122 | 71% helix, 6% strand | Q2N0S7 |
| D, I, J | PGV04 vh | protein | 125 | 9% helix, 47% strand | — |
| E, K, L | PGV04 vl | protein | 100 | 6% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 90 copies · chains A, D, E, C, B, I, K, G, F, J, L, H
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains E, K, L
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, E, B, K, F, L
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 | 980 | 0.84 | 0.85 | 93 | empty |
| 2 | 993 | 0.79 | 0.80 | 138 | NAG |
| 3 | 500 | 0.75 | 0.83 | 68 | NAG |
| 4 | 232 | 0.72 | 0.88 | 44 | empty |
| 5 | 668 | 0.71 | 0.78 | 84 | empty |
Interfaces
24 interfaces between chains.
- A–C · 2451 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 2403 Ų buried · 21 hydrogen bonds · protein-protein
- F–H · 2291 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 960 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 931 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 34 disulfide (N-glycosylation, disulfide).
Compared structures
- 6CRQ · Glutaraldehyde-treated BG505 SOSIP.664 Env in complex with PGV04 Fab · 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
- Every structure of UniProt Q2N0S5
- Every structure of UniProt Q2N0S7
- Elsewhere: RCSB PDB 6CRQ · PDBe 6CRQ · UniProt Q2N0S5 · UniProt Q2N0S7
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