MolNFT v1 · #16844 · protein
Fv structure of the IgE spe-7 in complex with acenaphthenequinone
1OAX · Immunoglobulin E: “Fv structure of the IgE spe-7 in complex with acenaphthenequinone”. X-ray diffraction, 1 ligand (ANQ), 7 pockets (best druggability 0.61). MolNFT v1 #16844 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1OAX
- Type
- protein
- Length
- 675 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin E
- Ligands
- ANQ
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J | Immunoglobulin E | protein | 122 | 7% helix, 52% strand | — |
| L, M, N | Immunoglobulin E | protein | 108 | 6% helix, 55% strand | — |
| O | Immunoglobulin E | protein | 107 | 3% helix, 51% strand | — |
Ligands and binding sites
- ANQ · Acenaphthenequinone · ligand · 2 copies · chains H, L, J, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.61 | 0.80 | 42 | ANQ |
| 2 | 152 | 0.54 | 0.80 | 28 | ANQ |
| 3 | 121 | 0.44 | 0.78 | 23 | empty |
| 4 | 103 | 0.44 | 0.79 | 20 | empty |
| 5 | 102 | 0.42 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- J–N · 881 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 879 Ų buried · 9 hydrogen bonds · protein-protein
- H–O · 297 Ų buried · 2 hydrogen bonds · protein-protein
- J–M · 184 Ų buried · 1 hydrogen bond · protein-protein
- L–O · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1OAX · Fv Structure of the IgE SPE-7 in complex with acenaphthenequi · 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 1OAX · PDBe 1OAX
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