Research workbench
Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to CH31 scfv in complex with crystallization chaperones 3H109L Fab and 35O22 scfv at 3.1 ångström
Analyse Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to CH31… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NNJ
- Type
- protein
- Length
- 1,461 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP41; 35O22 scfv heavy chain; 35O22 scfv light chain; Envelope…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP41 | protein | 127 | 56% helix, 6% strand | Q2N0S6 |
| D | 35O22 scfv heavy chain | protein | 128 | 2% helix, 41% strand | — |
| E | 35O22 scfv light chain | protein | 110 | 3% helix, 42% strand | — |
| G | Envelope glycoprotein GP120 | protein | 430 | 14% helix, 42% strand | Q2N0S6 |
| H | 3H109L Fab heavy chain | protein | 226 | 8% helix, 53% strand | — |
| L | 3H109L Fab light chain | protein | 210 | 6% helix, 49% strand | — |
| U | CH31 scfv heavy chain | protein | 129 | 5% helix, 41% strand | — |
| V | CH31 scfv light chain | protein | 101 | 0% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains B, D, G, L, V, H, U
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains D, E, H, L
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.84 | 0.85 | 106 | NAG |
| 2 | 65 | 0.69 | 0.96 | 28 | empty |
| 3 | 281 | 0.62 | 0.80 | 38 | empty |
| 4 | 242 | 0.57 | 0.78 | 26 | empty |
| 5 | 222 | 0.53 | 0.77 | 31 | empty |
Interfaces
11 interfaces between chains.
- B–G · 2746 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1885 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 891 Ų buried · 9 hydrogen bonds · protein-protein
- G–U · 867 Ų buried · 12 hydrogen bonds · protein-protein
- U–V · 629 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 6NNJ · Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in… · 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
- Every structure of UniProt Q2N0S6
- Elsewhere: RCSB PDB 6NNJ · PDBe 6NNJ · UniProt Q2N0S6
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