Research workbench
Structure of an HIV epitope scaffold in complex with neutralizing antibody B12 Fab
Analyse Structure of an HIV epitope scaffold in complex with neutralizing antibody B12… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RU8
- Type
- protein
- Length
- 715 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epitope scaffold 2BODX43; Antibody B12, heavy chain; Antibody B12, light chain
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Epitope scaffold 2BODX43 | protein | 277 | 39% helix, 14% strand | — |
| H | Antibody B12, heavy chain | protein | 225 | 8% helix, 48% strand | — |
| L | Antibody B12, light chain | protein | 213 | 5% helix, 54% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains X, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.78 | 0.81 | 71 | GOL |
| 2 | 291 | 0.54 | 0.75 | 39 | empty |
| 3 | 62 | 0.29 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1805 Ų buried · 13 hydrogen bonds · protein-protein
- X–H · 1025 Ų buried · 14 hydrogen bonds · protein-protein
- X–L · 129 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3RU8 · Structure of an HIV epitope scaffold in complex with neutralizing antibody b12 Fab · the same entry in another collection · chain X against X, 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 3RU8 · PDBe 3RU8
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