Research workbench
Crystal structure of a stabilized ds-SOSIP.6MUT BG505 GP140 HIV-1 env trimer, containing mutations I201C-P433C (ds), L154M, Y177W, N300M, N302M, T320L, I420M in complex with human antibodies PGT122 and 35O22 at 4.3 a
Analyse Crystal structure of a stabilized ds-SOSIP.6MUT BG505 GP140 HIV-1 env trimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UTF
- Type
- protein
- Length
- 1,453 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; PGT122 light chain; PGT122 heavy…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 | protein | 439 | 13% helix, 37% strand | Q2N0S6 |
| B | Envelope glycoprotein GP41 | protein | 123 | 53% helix, 7% strand | Q2N0S6 |
| L | PGT122 light chain | protein | 208 | 4% helix, 44% strand | — |
| H | PGT122 heavy chain | protein | 228 | 3% helix, 52% strand | — |
| D | 35022 heavy chain | protein | 242 | 2% helix, 47% strand | — |
| E | 35022 light chain | protein | 213 | 1% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 35 copies · chains G, B, D, L, H, E
- MAN · alpha-D-mannopyranose · sugar · 19 copies · chains D, E, G, L, H
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.71 | 0.85 | 40 | empty |
| 2 | 222 | 0.68 | 0.85 | 41 | NAG |
| 3 | 254 | 0.65 | 0.82 | 42 | NAG |
| 4 | 480 | 0.58 | 0.73 | 54 | empty |
| 5 | 289 | 0.55 | 0.76 | 37 | empty |
Interfaces
8 interfaces between chains.
- G–B · 2555 Ų buried · 21 hydrogen bonds · protein-protein
- L–H · 2015 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1758 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 414 Ų buried · 7 hydrogen bonds · protein-protein
- G–L · 366 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 5UTF · Crystal Structure of a Stabilized DS-SOSIP.6mut BG505 gp140 HIV-1 Env Trimer, Containing… · the same entry in another collection · chain G against G, 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 5UTF · PDBe 5UTF · UniProt Q2N0S6
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