Research workbench
Crystal structure of the germline-targeting HIV-1 GP120 engineered outer domain, eod-GT6
Analyse Crystal structure of the germline-targeting HIV-1 GP120 engineered outer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JPJ
- Type
- protein
- Length
- 658 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Germline-targeting HIV-1 GP120 engineered outer domain, eod-GT6
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Germline-targeting HIV-1 GP120 engineered outer domain, eod-GT6 | protein | 170 | 13% helix, 37% strand | — |
| B | Germline-targeting HIV-1 GP120 engineered outer domain, eod-GT6 | protein | 169 | 15% helix, 39% strand | — |
| C | Germline-targeting HIV-1 GP120 engineered outer domain, eod-GT6 | protein | 157 | 16% helix, 42% strand | — |
| D | Germline-targeting HIV-1 GP120 engineered outer domain, eod-GT6 | protein | 162 | 14% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.65 | 0.83 | 37 | empty |
| 2 | 302 | 0.62 | 0.79 | 40 | empty |
| 3 | 391 | 0.60 | 0.77 | 40 | empty |
| 4 | 113 | 0.38 | 0.74 | 23 | empty |
| 5 | 55 | 0.32 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 642 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 376 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 367 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4JPJ · Crystal structure of the germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6 · 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 4JPJ · PDBe 4JPJ
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