Research workbench
M1PRIME peptide from IgE bound by humanized antibody 47H4 Fab
Analyse M1PRIME peptide from IgE bound by humanized antibody 47H4 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HR5
- Type
- protein
- Length
- 1,797 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab H47H4 light chain; Fab H47H4 heavy chain; M1PRIME-derived peptide
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A, P, Q | Fab H47H4 light chain | protein | 219 | 5% helix, 52% strand | — |
| H, B, I, J | Fab H47H4 heavy chain | protein | 220 | 7% helix, 52% strand | — |
| R | M1PRIME-derived peptide | protein | 9 | 0% helix, 11% strand | — |
| S | M1PRIME-derived peptide | protein | 11 | 0% helix, 18% strand | — |
| T | M1PRIME-derived peptide | protein | 11 | 0% helix, 9% strand | — |
| V | M1PRIME-derived peptide | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, H, P, B, Q, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.70 | 0.77 | 76 | GOL |
| 2 | 683 | 0.69 | 0.77 | 76 | empty |
| 3 | 501 | 0.67 | 0.79 | 78 | GOL |
| 4 | 572 | 0.65 | 0.76 | 54 | empty |
| 5 | 424 | 0.65 | 0.78 | 40 | GOL |
Interfaces
28 interfaces between chains.
- L–H · 1995 Ų buried · 10 hydrogen bonds · protein-protein
- P–I · 1972 Ų buried · 15 hydrogen bonds · protein-protein
- Q–J · 1960 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1941 Ų buried · 16 hydrogen bonds · protein-protein
- B–Q · 585 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide (disulfide).
Compared structures
- 3HR5 · M1prime peptide from IgE bound by humanized antibody 47H4 Fab · the same entry in another collection · chain L against L, 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 3HR5 · PDBe 3HR5
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