MolNFT v1 · #77953 · protein
Structure of an HIV epitope scaffold in complex with neutralizing antibody B12 Fab
3RU8 · Epitope scaffold 2BODX43: “Structure of an HIV epitope scaffold in complex with neutralizing antibody B12 Fab”. X-ray diffraction, 3 pockets (best druggability 0.78). MolNFT v1 #77953 on GenesisL1: 3D structure, binding sites and…
- 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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