MolNFT v1 · #46491 · protein
Crystal structure of the 1E9 LEUH47TRP/ARGH100TRP Fab 5-beta- androstane-3,17-dione complex
2O5Z · Chimeric antibody Fab 1E9-DB3: “Crystal structure of the 1E9 LEUH47TRP/ARGH100TRP Fab 5-beta- androstane-3,17-dione complex”. X-ray diffraction, 2 ligands (ANO, SO4), 6 pockets (best druggability 0.63). MolNFT v1 #46491 on…
- PDB
- 2O5Z
- 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
- ANO, SO4
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Chimeric antibody Fab 1E9-DB3 | protein | 218 | 5% helix, 51% strand | — |
| H | Chimeric antibody Fab 1E9-DB3 | protein | 219 | 9% helix, 53% strand | — |
Ligands and binding sites
- ANO · 5-beta-androstane-3,17-dione · ligand · chains L, H
- SO4 · Sulfate ion · ion · 23 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.63 | 0.94 | 17 | empty |
| 2 | 544 | 0.59 | 0.73 | 69 | empty |
| 3 | 132 | 0.50 | 0.79 | 19 | ANO |
| 4 | 109 | 0.39 | 0.75 | 24 | empty |
| 5 | 72 | 0.32 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- L–H · 1762 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2O5Z · Crystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab 5-beta-androstane-3,17-dione complex · 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 2O5Z · PDBe 2O5Z
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