MolNFT v1 · #182254 · protein
Crystal structure of human IgE (2F10) in complex with der P 2.0103
7MLH · IgE light chain: “Crystal structure of human IgE (2F10) in complex with der P 2.0103”. X-ray diffraction, 2 ligands (SO4, CL), 8 pockets (best druggability 0.86). MolNFT v1 #182254 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7MLH
- Type
- protein
- Length
- 1,099 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgE light chain; Der P 2 variant 3; IgE heavy chain
- UniProt
- I2CMD6
- Ligands
- SO4, CL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IgE light chain | protein | 209 | 6% helix, 52% strand | — |
| B, F | Der P 2 variant 3 | protein | 129 | 3% helix, 53% strand | I2CMD6 |
| C | IgE heavy chain | protein | 207 | 6% helix, 51% strand | — |
| D | IgE light chain | protein | 210 | 6% helix, 52% strand | — |
| E | IgE heavy chain | protein | 215 | 7% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, E, C, D
- CL · Chloride ion · ion · 3 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.86 | 0.92 | 58 | empty |
| 2 | 453 | 0.86 | 0.93 | 58 | empty |
| 3 | 468 | 0.58 | 0.73 | 56 | empty |
| 4 | 399 | 0.54 | 0.73 | 57 | empty |
| 5 | 315 | 0.53 | 0.74 | 47 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1649 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1623 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 591 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 575 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 7MLH · Crystal structure of human IgE (2F10) in complex with Der p 2.0103 · the same entry in another collection · chain A against A, 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
- Every structure of UniProt I2CMD6
- Elsewhere: RCSB PDB 7MLH · PDBe 7MLH · UniProt I2CMD6
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