MolNFT v1 · #168516 · protein
Crystal structure of HIV-1 MI369 rns-DS.SOSIP prefusion env trimer in complex with human antibodies 3H109L and 35O22 at 3.5 ångström
6WIX · Envelope glycoprotein GP41: “Crystal structure of HIV-1 MI369 rns-DS.SOSIP prefusion env trimer in complex with human antibodies 3H109L…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 16 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 6WIX
- Type
- protein
- Length
- 1,215 residues
- Chains
- 6
- 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…
- Ligands
- NAG, MAN, BMA
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP41 | protein | 120 | 57% helix, 6% strand | — |
| D | 35O22 scfv heavy chain | protein | 128 | 5% helix, 48% strand | — |
| E | 35O22 scfv light chain | protein | 105 | 3% helix, 32% strand | — |
| G | Envelope glycoprotein GP120 | protein | 425 | 12% helix, 42% strand | — |
| H | 3H109L Fab heavy chain | protein | 226 | 7% helix, 49% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 6% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains B, D, G, H
- MAN · alpha-D-mannopyranose · sugar · 10 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
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.69 | 0.83 | 57 | NAG |
| 2 | 327 | 0.64 | 0.80 | 44 | empty |
| 3 | 281 | 0.57 | 0.77 | 25 | empty |
| 4 | 193 | 0.50 | 0.76 | 28 | empty |
| 5 | 76 | 0.39 | 0.78 | 17 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2645 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 1962 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 891 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 408 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 396 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 6WIX · Crystal Structure of HIV-1 MI369 RnS-DS.SOSIP Prefusion Env Trimer in Complex with Human… · 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
- Elsewhere: RCSB PDB 6WIX · PDBe 6WIX
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