MolNFT v1 · #46489 · protein
Crystal structure of 1E9 LEUH47TRP/ARGH100TRP, an engineered diels- alderase Fab with nm steroid-binding affinity
2O5X · Chimeric antibody Fab 1E9-DB3: “Crystal structure of 1E9 LEUH47TRP/ARGH100TRP, an engineered diels- alderase Fab with nm steroid-binding…”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.63). MolNFT v1 #46489 on…
- PDB
- 2O5X
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric antibody Fab 1E9-DB3
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Chimeric antibody Fab 1E9-DB3 | protein | 218 | 6% helix, 51% strand | — |
| H | Chimeric antibody Fab 1E9-DB3 | protein | 219 | 11% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains L, H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.63 | 0.74 | 67 | empty |
| 2 | 127 | 0.52 | 0.80 | 17 | TRS |
| 3 | 113 | 0.40 | 0.76 | 25 | empty |
| 4 | 98 | 0.33 | 0.73 | 23 | empty |
| 5 | 50 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- L–H · 1776 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2O5X · Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM… · 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 2O5X · PDBe 2O5X
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