Research workbench
2F5 epitope scaffold elicited anti-HIV-1 monoclonal antibody 6A7 in complex with HIV-1 GP41
Analyse 2F5 epitope scaffold elicited anti-HIV-1 monoclonal antibody 6A7 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LEY
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6A7 antibody heavy chain; 6A7 antibody light chain; Envelope glycoprotein GP41
- UniProt
- Q9IJQ0
- Ligands
- ZN, NH2
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 6A7 antibody heavy chain | protein | 217 | 4% helix, 54% strand | — |
| L | 6A7 antibody light chain | protein | 216 | 7% helix, 53% strand | — |
| P | Envelope glycoprotein GP41 | protein | 8 | 0% helix, 0% strand | Q9IJQ0 |
Ligands and binding sites
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 | 485 | 0.59 | 0.74 | 56 | empty |
| 2 | 95 | 0.40 | 0.77 | 23 | empty |
| 3 | 83 | 0.32 | 0.73 | 17 | empty |
| 4 | 64 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1984 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 333 Ų buried · 8 hydrogen bonds · protein-protein
- L–P · 325 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3LEY · 2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 6a7 in complex with HIV-1… · 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
- Every structure of UniProt Q9IJQ0
- Elsewhere: RCSB PDB 3LEY · PDBe 3LEY · UniProt Q9IJQ0
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