Research workbench
Crystal structure of ALPHA1-antichymotrypsin variant dbs-I5: a MMP14- cleavable drug-binding serpin for doxycycline
Analyse Crystal structure of ALPHA1-antichymotrypsin variant dbs-I5: a MMP14- cleavable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OM3
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1-antichymotrypsin
- UniProt
- P01011
- Ligands
- DXT
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1-antichymotrypsin | protein | 335 | 36% helix, 36% strand | P01011 |
| B | Alpha-1-antichymotrypsin | protein | 33 | 0% helix, 58% strand | P01011 |
Ligands and binding sites
- DXT · (4s,4ar,5s,5ar,6r,12as)-4-(dimethylamino)-3,5,10,12,12A-pentahydroxy-6-methyl-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.53 | 0.81 | 24 | DXT |
| 2 | 77 | 0.36 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2449 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5OM3 · Crystal structure of Alpha1-antichymotrypsin variant DBS-I5: a MMP14-cleavable… · the same entry in another collection · chain A against A, 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 0.93
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 5OM3 · PDBe 5OM3 · UniProt P01011
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