Research workbench
Crystal structure of ALPHA1-antichymotrypsin variant dbs-I-ALLO2: a MMP9-cleavable drug-binding serpin for doxycycline
Analyse Crystal structure of ALPHA1-antichymotrypsin variant dbs-I-ALLO2: a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OM6
- Type
- protein
- Length
- 752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1-antichymotrypsin
- UniProt
- P01011
- Ligands
- CL
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1-antichymotrypsin | protein | 339 | 35% helix, 36% strand | P01011 |
| B, D | Alpha-1-antichymotrypsin | protein | 39 | 0% helix, 41% strand | P01011 |
| C | Alpha-1-antichymotrypsin | protein | 335 | 33% helix, 35% strand | P01011 |
Ligands and binding sites
- CL · Chloride ion · ion · chains C, D
- CIT · Citric acid · additive · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.51 | 0.76 | 30 | empty |
| 2 | 111 | 0.47 | 0.79 | 17 | empty |
| 3 | 117 | 0.46 | 0.78 | 18 | empty |
| 4 | 101 | 0.41 | 0.77 | 18 | CIT |
| 5 | 56 | 0.27 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2466 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2430 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 209 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5OM6 · Crystal structure of Alpha1-antichymotrypsin variant DBS-I-allo2: a MMP9-cleavable… · the same entry in another collection · chain D against D, TM-score 1.00
- P01011 · AlphaFold monomer V2.0 prediction for alpha-1-antichymotrypsin (P01011) · a predicted model of the same protein · chain A against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01011
- Elsewhere: RCSB PDB 5OM6 · PDBe 5OM6 · UniProt P01011
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