MolNFT v1 · #14734 · protein
Crystal structure of the complex of the Fab fragment of esterolytic antibody MS5-393 and a transition-state analog
1MJ7 · Immunoglobulin MS5-393: “Crystal structure of the complex of the Fab fragment of esterolytic antibody MS5-393 and a transition-state…”. X-ray diffraction, 1 ligand (HAL), 3 pockets (best druggability 0.71). MolNFT v1 #14734 on…
- PDB
- 1MJ7
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin MS5-393
- Ligands
- HAL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin MS5-393 | protein | 218 | 5% helix, 50% strand | — |
| H | Immunoglobulin MS5-393 | protein | 193 | 8% helix, 55% strand | — |
Ligands and binding sites
- HAL · N-{[2-({[1-(4-carboxybutanoyl)amino]-2-phenylethyl}-hydroxyphosphinyl)oxy]acetyl}-2-phenylethylamine · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.71 | 0.77 | 65 | empty |
| 2 | 146 | 0.60 | 0.83 | 21 | HAL |
| 3 | 69 | 0.33 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- L–H · 1638 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MJ7 · Crystal Structure Of The Complex Of The Fab fragment of Esterolytic Antibody MS5-393 and… · 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 1MJ7 · PDBe 1MJ7
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