Research workbench
Chimpanzee SIV env trimeric ectodomain.
Analyse Chimpanzee SIV env trimeric ectodomain. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OHY
- Type
- protein
- Length
- 1,701 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160
- UniProt
- Q1A234
- Ligands
- NAG, FUC, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Envelope glycoprotein GP160 | protein | 447 | 14% helix, 36% strand | Q1A234 |
| B, E, F | Envelope glycoprotein GP160 | protein | 120 | 58% helix, 1% strand | Q1A234 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 96 copies · chains A, B, C, E, D, F
- FUC · alpha-L-fucopyranose · sugar · 15 copies · chains A, B, C, E, D, F
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, C, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.82 | 0.93 | 45 | empty |
| 2 | 63 | 0.72 | 0.97 | 23 | empty |
| 3 | 894 | 0.72 | 0.76 | 79 | empty |
| 4 | 344 | 0.67 | 0.81 | 47 | empty |
| 5 | 561 | 0.64 | 0.76 | 60 | empty |
Interfaces
12 interfaces between chains.
- C–E · 2740 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2730 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 2719 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 920 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 919 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 6OHY · Chimpanzee SIV Env trimeric ectodomain. · 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 Q1A234
- Elsewhere: RCSB PDB 6OHY · PDBe 6OHY · UniProt Q1A234
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