Research workbench
Crystal structure of unliganded HIV-1 clade B strain YU2 GP120 core
Analyse Crystal structure of unliganded HIV-1 clade B strain YU2 GP120 core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TGQ
- Type
- protein
- Length
- 1,344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 YU2 GP120
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HIV-1 YU2 GP120 | protein | 336 | 15% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.83 | 0.86 | 111 | NAG |
| 2 | 544 | 0.65 | 0.76 | 56 | empty |
| 3 | 292 | 0.60 | 0.79 | 43 | empty |
| 4 | 104 | 0.59 | 0.86 | 24 | empty |
| 5 | 106 | 0.59 | 0.86 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1033 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 191 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 54 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 25 glycan (disulfide, N-glycosylation).
Compared structures
- 3TGQ · Crystal structure of unliganded HIV-1 clade B strain YU2 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
- Elsewhere: RCSB PDB 3TGQ · PDBe 3TGQ
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