Research workbench
Fv structure of the IgE spe-7 in complex with dnp-ser (immunising hapten)
Analyse Fv structure of the IgE spe-7 in complex with dnp-ser (immunising hapten) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OAU
- Type
- protein
- Length
- 685 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin E
- Ligands
- SER, DNF
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J | Immunoglobulin E | protein | 122 | 10% helix, 53% strand | — |
| I | Immunoglobulin E | protein | 21 | 0% helix, 0% strand | — |
| K | Immunoglobulin E | protein | 22 | 0% helix, 0% strand | — |
| L, N | Immunoglobulin E | protein | 108 | 6% helix, 55% strand | — |
| M | Immunoglobulin E | protein | 90 | 7% helix, 44% strand | — |
| O | Immunoglobulin E | protein | 92 | 7% helix, 51% strand | — |
Ligands and binding sites
- SER · Serine · ligand · 2 copies · chains H, L, O, J, M, N
- DNF · 2,4-dinitrophenol · ligand · 2 copies · chains H, L, J, N
- IMD · Imidazole · additive · 2 copies · chains H, L, J, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.60 | 0.78 | 40 | SER, DNF |
| 2 | 156 | 0.53 | 0.80 | 30 | SER, DNF |
| 3 | 122 | 0.42 | 0.76 | 19 | empty |
| 4 | 93 | 0.35 | 0.74 | 16 | empty |
| 5 | 63 | 0.26 | 0.72 | 16 | empty |
Interfaces
8 interfaces between chains.
- H–L · 865 Ų buried · 6 hydrogen bonds · protein-protein
- J–N · 863 Ų buried · 7 hydrogen bonds · protein-protein
- H–O · 235 Ų buried · 0 hydrogen bonds · protein-protein
- I–M · 231 Ų buried · 0 hydrogen bonds · protein-protein
- K–O · 230 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1OAU · Fv Structure of the IgE SPE-7 in complex with DNP-Ser (immunising hapten) · the same entry in another collection · chain O against O, 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 1OAU · PDBe 1OAU
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