Research workbench
Crystal structure of 1E9 PHEL89SER/LEUH47TRP/METH100BPHE, an engineered diels-alderase Fab with modified specificity and catalytic activity
Analyse Crystal structure of 1E9 PHEL89SER/LEUH47TRP/METH100BPHE, an engineered… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O2V
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric antibody Fab 1E9, light chain; Chimeric antibody Fab 1E9, heavy chain
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Chimeric antibody Fab 1E9, light chain | protein | 218 | 6% helix, 51% strand | — |
| H | Chimeric antibody Fab 1E9, heavy chain | protein | 219 | 9% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains L, H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 10 copies · chains L, H
- FLC · Citrate anion · additive · 3 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.59 | 0.73 | 56 | empty |
| 2 | 106 | 0.49 | 0.81 | 16 | empty |
| 3 | 146 | 0.44 | 0.75 | 28 | SO4 |
| 4 | 110 | 0.41 | 0.76 | 24 | empty |
| 5 | 97 | 0.34 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- L–H · 1755 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3O2V · Crystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engineered Diels-Alderase… · 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 3O2V · PDBe 3O2V
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