Research workbench
Crystal structure of chimeric germ-line precursor of NIH45-46 Fab in complex with GP120 of 93TH057 HIV-1
Analyse Crystal structure of chimeric germ-line precursor of NIH45-46 Fab in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JDT
- Type
- protein
- Length
- 751 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP120; Fab heavy chain; Fab light chain
- Ligands
- NAG, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | GP120 | protein | 336 | 18% helix, 36% strand | — |
| H | Fab heavy chain | protein | 209 | 10% helix, 53% strand | — |
| L | Fab light chain | protein | 206 | 6% helix, 51% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.70 | 0.80 | 45 | SO4 |
| 2 | 304 | 0.61 | 0.79 | 36 | empty |
| 3 | 56 | 0.52 | 0.88 | 22 | empty |
| 4 | 63 | 0.49 | 0.84 | 20 | empty |
| 5 | 65 | 0.46 | 0.83 | 21 | NAG |
Interfaces
3 interfaces between chains.
- H–L · 1621 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 744 Ų buried · 21 hydrogen bonds · protein-protein
- G–L · 211 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4JDT · Crystal structure of chimeric germ-line precursor of NIH45-46 Fab in complex with gp120… · the same entry in another collection · chain G against G, 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 4JDT · PDBe 4JDT
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