MolNFT v1 · #14735 · protein
High resolution crystal structure of the Fab fragment of the esterolytic antibody MS6-126
1MJ8 · Immunoglobulin MS6-126: “High resolution crystal structure of the Fab fragment of the esterolytic antibody MS6-126”. X-ray diffraction, 1 ligand (PO4), 6 pockets (best druggability 0.67). MolNFT v1 #14735 on GenesisL1: 3D structure…
- PDB
- 1MJ8
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin MS6-126
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin MS6-126 | protein | 214 | 6% helix, 50% strand | — |
| H | Immunoglobulin MS6-126 | protein | 216 | 8% helix, 51% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains L, H
- GOL · Glycerol · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.67 | 0.88 | 26 | PO4, GOL |
| 2 | 708 | 0.67 | 0.75 | 58 | PO4 |
| 3 | 170 | 0.52 | 0.79 | 27 | empty |
| 4 | 101 | 0.50 | 0.82 | 28 | GOL |
| 5 | 104 | 0.35 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- L–H · 1979 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1MJ8 · High Resolution Crystal Structure Of The Fab Fragment of The Esterolytic Antibody MS6-126 · 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 1MJ8 · PDBe 1MJ8
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