MolNFT v1 · #11461 · protein
Crystal structure of Fab-estradiol complexes
1JNH · Monoclonal anti-estradiol 10G6D6 Fab light chain: “Crystal structure of Fab-estradiol complexes”. X-ray diffraction, 1 ligand (ECO), 20 pockets (best druggability 0.76). MolNFT v1 #11461 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1JNH
- Type
- protein
- Length
- 1,688 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal anti-estradiol 10G6D6 Fab light chain; Monoclonal anti-estradiol 10G6D6 Fab…
- Ligands
- ECO
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Monoclonal anti-estradiol 10G6D6 Fab light chain | protein | 208 | 8% helix, 56% strand | — |
| B, D, F, H | Monoclonal anti-estradiol 10G6D6 Fab heavy chain | protein | 214 | 6% helix, 54% strand | — |
Ligands and binding sites
- ECO · Estradiol-6 carboxyl-methyl-oxime · ligand · 4 copies · chains A, B, F, C, D, H, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.76 | 0.79 | 95 | empty |
| 2 | 147 | 0.62 | 0.85 | 24 | ECO |
| 3 | 460 | 0.60 | 0.75 | 48 | empty |
| 4 | 129 | 0.57 | 0.84 | 24 | ECO |
| 5 | 361 | 0.53 | 0.73 | 40 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1935 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1925 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1920 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1919 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 275 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1JNH · Crystal Structure of Fab-Estradiol Complexes · 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
- Elsewhere: RCSB PDB 1JNH · PDBe 1JNH
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