Research workbench
Crystal structure of kd-247 Fab, an anti-V3 antibody that inhibits HIV-1 entry
Analyse Crystal structure of kd-247 Fab, an anti-V3 antibody that inhibits HIV-1 entry in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NTC
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 219 | 6% helix, 51% strand | — |
| H | Fab heavy chain | protein | 221 | 7% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains L, H
- EDO · 1,2-ethanediol · additive · 12 copies · chains L, H
- ACT · Acetate ion · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.68 | 0.75 | 71 | EDO |
| 2 | 187 | 0.48 | 0.75 | 24 | empty |
| 3 | 69 | 0.36 | 0.77 | 16 | EDO |
| 4 | 59 | 0.28 | 0.74 | 14 | empty |
| 5 | 56 | 0.26 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- L–H · 1961 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3NTC · Crystal structure of KD-247 Fab, an anti-V3 antibody that inhibits HIV-1 Entry · the same entry in another collection · chain L against L, 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 3NTC · PDBe 3NTC
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.