Research workbench
Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer in complex with V3 loop-targeting antibody PGT122 Fab and fusion peptide-targeting antibody VRC34.01 Fab
Analyse Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I8H
- Type
- protein
- Length
- 2,915 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 SOSIP.664 GP120; BG505 SOSIP.664 GP41; PGT122 Fab light chain; VRC34.01 Fab heavy…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BG505 SOSIP.664 GP120 | protein | 455 | 11% helix, 36% strand | Q2N0S6 |
| B, D | BG505 SOSIP.664 GP41 | protein | 132 | 52% helix, 7% strand | Q2N0S6 |
| C | BG505 SOSIP.664 GP120 | protein | 450 | 12% helix, 37% strand | Q2N0S6 |
| L, J | PGT122 Fab light chain | protein | 210 | 5% helix, 47% strand | — |
| E, G | VRC34.01 Fab heavy chain | protein | 223 | 9% helix, 50% strand | — |
| F, H | VRC34.01 Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| I, K | PGT122 Fab heavy chain | protein | 228 | 5% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 70 copies · chains A, B, E, F, J, I, C, G, D, H, L, K
- MAN · alpha-D-mannopyranose · sugar · 33 copies · chains F, A, I, J, H, C, L, K
- BMA · beta-D-mannopyranose · sugar · 13 copies · chains F, K, I, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.72 | 0.76 | 105 | empty |
| 2 | 73 | 0.71 | 0.96 | 27 | empty |
| 3 | 425 | 0.70 | 0.81 | 64 | NAG |
| 4 | 60 | 0.67 | 0.95 | 26 | empty |
| 5 | 261 | 0.66 | 0.82 | 49 | NAG |
Interfaces
22 interfaces between chains.
- C–D · 2582 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2566 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 2049 Ų buried · 15 hydrogen bonds · protein-protein
- L–K · 2028 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1863 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 glycan, 38 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 5I8H · Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3… · the same entry in another collection · chain A against A, 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 5I8H · PDBe 5I8H · UniProt Q2N0S6
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