MolNFT v2 · #159267 · protein
Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to N6 FR3-03 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.2 Angstrom
6NM6 · Envelope glycoprotein gp41: “Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to N6 FR3-03 scFv in Complex with…”. X-ray diffraction at 2.739, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.74).…
- PDB
- 6NM6
- Type
- protein
- Length
- 1,456 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.739
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- Envelope glycoprotein gp41; 35O22 scFv heavy chain; 35O22 scFv light chain; Envelope…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.739 · 8 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein gp41 | protein | 126 | 53% helix, 7% strand | Q2N0S6 |
| D | 35O22 scFv heavy chain | protein | 128 | 2% helix, 38% strand | — |
| E | 35O22 scFv light chain | protein | 110 | 3% helix, 44% strand | — |
| G | Envelope glycoprotein gp120 | protein | 429 | 11% helix, 41% strand | Q2N0S6 |
| H | 3H109L Fab heavy chain | protein | 226 | 7% helix, 51% strand | — |
| L | 3H109L Fab light chain | protein | 210 | 3% helix, 45% strand | — |
| U | N6 FR3-03 heavy chain | protein | 128 | 8% helix, 48% strand | — |
| V | N6 FR3-03 light chain | protein | 99 | 0% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains B, D, G, L, U, V, H, E
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains D, E, H, L
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, E, G, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.74 | 0.82 | 76 | empty |
| 2 | 216 | 0.66 | 0.84 | 44 | NAG |
| 3 | 251 | 0.60 | 0.80 | 35 | empty |
| 4 | 209 | 0.60 | 0.81 | 27 | empty |
| 5 | 221 | 0.52 | 0.76 | 30 | empty |
Interfaces
11 interfaces between chains.
- B–G · 2718 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1899 Ų buried · 11 hydrogen bonds · protein-protein
- G–U · 1054 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 890 Ų buried · 7 hydrogen bonds · protein-protein
- U–V · 706 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 6NM6 · Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to N6 FR3-03 scfv… · 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 6NM6 · PDBe 6NM6 · UniProt Q2N0S6
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