Research workbench
1.22 ångström resolution crystal structure of the Fab fragment of esterolytic antibody MS6-12
Analyse 1.22 ångström resolution crystal structure of the Fab fragment of esterolytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MJU
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin MS6-12
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin MS6-12 | protein | 219 | 5% helix, 49% strand | — |
| H | Immunoglobulin MS6-12 | protein | 212 | 7% helix, 53% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 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 | 731 | 0.67 | 0.75 | 57 | GOL |
| 2 | 99 | 0.67 | 0.90 | 19 | empty |
| 3 | 83 | 0.50 | 0.83 | 24 | empty |
| 4 | 132 | 0.45 | 0.77 | 27 | empty |
| 5 | 72 | 0.31 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- L–H · 2027 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 1MJU · 1.22 ångström resolution crystal structure of the Fab fragment of esterolytic antibody… · 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 1MJU · PDBe 1MJU
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