MolNFT v1 · #96638 · protein
Crystal structure of the germline-targeting HIV-1 GP120 engineered outer domain eod-GT6 in complex with a putative VRC01 germline precursor Fab
4JPK · Putative VRC01 germline precursor Fab heavy chain: “Crystal structure of the germline-targeting HIV-1 GP120 engineered outer domain eod-GT6 in complex with a…”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.54).…
- PDB
- 4JPK
- Type
- protein
- Length
- 598 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative VRC01 germline precursor Fab heavy chain; Putative VRC01 germline precursor Fab…
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Putative VRC01 germline precursor Fab heavy chain | protein | 221 | 10% helix, 51% strand | — |
| L | Putative VRC01 germline precursor Fab light chain | protein | 208 | 6% helix, 51% strand | — |
| A | Germline-targeting HIV-1 GP120 engineered outer domain, eod-GT6 | protein | 169 | 21% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.54 | 0.74 | 49 | empty |
| 2 | 135 | 0.51 | 0.80 | 25 | empty |
| 3 | 120 | 0.48 | 0.80 | 21 | empty |
| 4 | 129 | 0.44 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1872 Ų buried · 18 hydrogen bonds · protein-protein
- H–A · 870 Ų buried · 22 hydrogen bonds · protein-protein
- L–A · 313 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4JPK · Crystal structure of the germline-targeting HIV-1 gp120 engineered outer domain eOD-GT6… · the same entry in another collection · chain H against H, 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 4JPK · PDBe 4JPK
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