Research workbench
Cryo-EM structure of stabilized HIV-1 env trimer CAP256.WK34.C80 SOSIP.RNS2
Analyse Cryo-EM structure of stabilized HIV-1 env trimer CAP256.WK34.C80 SOSIP.RNS2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VRW
- Type
- protein
- Length
- 1,671 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A, D | Envelope glycoprotein GP120 | protein | 433 | 9% helix, 37% strand | — |
| B, C, E | Envelope glycoprotein GP41 | protein | 124 | 51% helix, 6% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains G, A, D, B, C, E
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains G, A, D
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.85 | 0.89 | 83 | empty |
| 2 | 303 | 0.77 | 0.89 | 42 | empty |
| 3 | 202 | 0.69 | 0.86 | 37 | NAG |
| 4 | 1155 | 0.69 | 0.74 | 92 | empty |
| 5 | 195 | 0.68 | 0.86 | 39 | NAG |
Interfaces
12 interfaces between chains.
- A–C · 2574 Ų buried · 15 hydrogen bonds · protein-protein
- G–B · 2569 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 2567 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1162 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 1141 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 6VRW · Cryo-EM structure of stabilized HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2 · 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
- Elsewhere: RCSB PDB 6VRW · PDBe 6VRW
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