Research workbench
Improved structure of the unliganded simian immunodeficiency virus GP120 core
Analyse Improved structure of the unliganded simian immunodeficiency virus GP120 core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FUS
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exterior membrane glycoprotein GP120
- UniProt
- Q07374
- Ligands
- NAG, BMA, MAN, FUL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exterior membrane glycoprotein GP120 | protein | 304 | 12% helix, 17% strand | Q07374 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A
- FUL · beta-L-fucopyranose · sugar · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.85 | 0.86 | 124 | empty |
| 2 | 504 | 0.76 | 0.83 | 54 | empty |
| 3 | 326 | 0.64 | 0.80 | 36 | empty |
| 4 | 62 | 0.61 | 0.91 | 17 | empty |
| 5 | 174 | 0.53 | 0.79 | 24 | empty |
Modifications
Observed in the structure: 13 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 3FUS · Improved Structure of the Unliganded Simian Immunodeficiency Virus gp120 Core · 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 Q07374
- Elsewhere: RCSB PDB 3FUS · PDBe 3FUS · UniProt Q07374
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