Research workbench
Crystal structure of non-neutralizing version of 4E10 (wdwd) with epitope bound
Analyse Crystal structure of non-neutralizing version of 4E10 (wdwd) with epitope bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CIL
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 4E10 heavy chain; Fab 4E10 light chain; Peptide from the mper region of the env…
- Ligands
- CL
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab 4E10 heavy chain | protein | 220 | 8% helix, 54% strand | — |
| L | Fab 4E10 light chain | protein | 212 | 7% helix, 49% strand | — |
| P | Peptide from the mper region of the env protein of HIV-1 | protein | 13 | 85% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains H, L
- GOL · Glycerol · additive · 2 copies · chains H, L
- ACT · Acetate ion · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.60 | 0.74 | 54 | ACT |
| 2 | 122 | 0.43 | 0.77 | 23 | empty |
| 3 | 68 | 0.28 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1636 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 583 Ų buried · 5 hydrogen bonds · protein-protein
- L–P · 217 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5CIL · Crystal Structure of non-neutralizing version of 4E10 (WDWD) with epitope bound · 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 5CIL · PDBe 5CIL
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