Research workbench
The structure of the complex of the Fab fragment of the esterolytic antibody MS6-164 and a transition-state analog
Analyse The structure of the complex of the Fab fragment of the esterolytic antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MH5
- Type
- protein
- Length
- 771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin MS6-164
- Ligands
- HAL, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin MS6-164 | protein | 197 | 2% helix, 48% strand | — |
| B | Immunoglobulin MS6-164 | protein | 172 | 5% helix, 47% strand | — |
| L | Immunoglobulin MS6-164 | protein | 212 | 6% helix, 49% strand | — |
| H | Immunoglobulin MS6-164 | protein | 190 | 6% helix, 48% strand | — |
Ligands and binding sites
- HAL · N-{[2-({[1-(4-carboxybutanoyl)amino]-2-phenylethyl}-hydroxyphosphinyl)oxy]acetyl}-2-phenylethylamine · ligand · 2 copies · chains A, B, L, H
- SO4 · Sulfate ion · ion · 2 copies · chains B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.65 | 0.74 | 53 | empty |
| 2 | 141 | 0.63 | 0.86 | 26 | HAL |
| 3 | 584 | 0.62 | 0.74 | 54 | empty |
| 4 | 136 | 0.61 | 0.84 | 24 | HAL |
Interfaces
2 interfaces between chains.
- L–H · 1637 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1552 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1MH5 · The Structure Of The Complex Of The Fab Fragment Of The Esterolytic Antibody MS6-164 and… · 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 1MH5 · PDBe 1MH5
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