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Crystal structure analysis of anti-HIV-1 V3-Fab F425-B4E8 in complex with a V3-peptide
Analyse Crystal structure analysis of anti-HIV-1 V3-Fab F425-B4E8 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QSC
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab F425-B4E8, light chain; Fab F425-B4E8, heavy chain; Envelope glycoprotein GP120
- UniProt
- P05877
- Ligands
- NAG, BMA, ZN, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab F425-B4E8, light chain | protein | 215 | 5% helix, 50% strand | — |
| H | Fab F425-B4E8, heavy chain | protein | 211 | 7% helix, 54% strand | — |
| P | Envelope glycoprotein GP120 | protein | 15 | 0% helix, 40% strand | P05877 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 4 copies · chains L, H
- CL · Chloride ion · ion · 4 copies · chains L, H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.67 | 0.75 | 69 | empty |
| 2 | 112 | 0.37 | 0.74 | 18 | empty |
| 3 | 68 | 0.30 | 0.74 | 20 | empty |
| 4 | 84 | 0.30 | 0.72 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1820 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 352 Ų buried · 3 hydrogen bonds · protein-protein
- L–P · 253 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2QSC · Crystal structure analysis of anti-HIV-1 V3-Fab F425-B4e8 in complex with a V3-peptide · 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
- Every structure of UniProt P05877
- Elsewhere: RCSB PDB 2QSC · PDBe 2QSC · UniProt P05877
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