Research workbench
Cryo-EM structure of shiv-elicited RHA1.V2.01 in complex with HIV-1 env BG505 ds-SOSIP.664
Analyse Cryo-EM structure of shiv-elicited RHA1.V2.01 in complex with HIV-1 env BG505… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XRT
- Type
- protein
- Length
- 1,947 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41; VRC01.23…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 446 | 11% helix, 37% strand | Q2N0S6 |
| B | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 124 | 49% helix, 4% strand | Q2N0S6 |
| E | Envelope glycoprotein GP160 | protein | 446 | 10% helix, 39% strand | Q2N0S6 |
| F | Envelope glycoprotein GP160 | protein | 445 | 10% helix, 36% strand | Q2N0S6 |
| C | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 126 | 40% helix, 4% strand | Q2N0S6 |
| A | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 122 | 55% helix, 2% strand | Q2N0S6 |
| H | VRC01.23 heavy chain | protein | 133 | 5% helix, 38% strand | — |
| L | VRC01.23 light chain | protein | 105 | 0% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 76 copies · chains G, H, E, L, F, B, C, A
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains H, E, G, F, L
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.82 | 0.94 | 40 | empty |
| 2 | 1088 | 0.79 | 0.80 | 85 | empty |
| 3 | 1175 | 0.76 | 0.78 | 112 | empty |
| 4 | 207 | 0.76 | 0.91 | 43 | NAG |
| 5 | 64 | 0.74 | 0.97 | 19 | empty |
Interfaces
18 interfaces between chains.
- F–A · 2737 Ų buried · 11 hydrogen bonds · protein-protein
- E–C · 2726 Ų buried · 10 hydrogen bonds · protein-protein
- G–B · 2692 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 1019 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 879 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 glycan, 38 disulfide, 1 modified (N-glycosylation, disulfide, sulfation).
Compared structures
- 6XRT · Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664 · 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 6XRT · PDBe 6XRT · UniProt Q2N0S6
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