MolNFT v1 · #16838 · protein
Fv IgE spe-7 in complex with alizarin red
1OAR · Immunoglobulin E: “Fv IgE spe-7 in complex with alizarin red”. X-ray diffraction, 3 ligands (AZN, NA, CL), 8 pockets (best druggability 0.59). MolNFT v1 #16838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1OAR
- Type
- protein
- Length
- 839 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin E; Immunoglobuling E
- Ligands
- AZN, NA, CL
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J | Immunoglobulin E | protein | 122 | 7% helix, 53% strand | — |
| I | Immunoglobulin E | protein | 88 | 0% helix, 53% strand | — |
| K | Immunoglobulin E | protein | 82 | 0% helix, 55% strand | — |
| L, N | Immunoglobuling E | protein | 108 | 6% helix, 57% strand | — |
| M | Immunoglobuling E | protein | 103 | 6% helix, 55% strand | — |
| O | Immunoglobuling E | protein | 106 | 6% helix, 58% strand | — |
Ligands and binding sites
- AZN · Alizarin red · ligand · 4 copies · chains H, L, O, I, M, J, N, K
- NA · Sodium ion · metal · 6 copies · chains L, N, J, M
- CL · Chloride ion · ion · 8 copies · chains J, H, L, M, N, O
- DMS · Dimethyl sulfoxide · additive · 24 copies · chains H, O, J, M, L, N
- CAC · Cacodylate ion · additive · 2 copies · chains H, L, J, N
- EDO · 1,2-ethanediol · additive · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.59 | 0.80 | 41 | DMS, AZN |
| 2 | 138 | 0.54 | 0.81 | 26 | AZN |
| 3 | 50 | 0.44 | 0.83 | 15 | AZN |
| 4 | 156 | 0.43 | 0.75 | 28 | DMS, CL |
| 5 | 95 | 0.41 | 0.77 | 20 | empty |
Interfaces
9 interfaces between chains.
- J–N · 884 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 875 Ų buried · 7 hydrogen bonds · protein-protein
- K–O · 853 Ų buried · 7 hydrogen bonds · protein-protein
- I–M · 848 Ų buried · 7 hydrogen bonds · protein-protein
- H–O · 245 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1OAR · Fv IgE SPE-7 in complex with Alizarin Red · the same entry in another collection · chain N against N, 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 1OAR · PDBe 1OAR
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