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Crystal structures of alpha-lytic protease complexes with irreversibly bound phosphonate esters
Analyse Crystal structures of alpha-lytic protease complexes with irreversibly bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P11
- Type
- protein
- Length
- 205 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-lytic protease; Phosphonate ester inhibitor a; Phosphonate ester inhibitor…
- EC
- 3.4.21.12
- UniProt
- P00778
- Ligands
- BOC, PVA, LAC, SO4
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Alpha-lytic protease (EC 3.4.21.12) | protein | 198 | 7% helix, 55% strand | P00778 |
| P | Phosphonate ester inhibitor a | protein | 4 | 0% helix, 25% strand | — |
| I | Phosphonate ester inhibitor B(TRANSITION state) | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- BOC · Tert-butyl hydrogen carbonate · ligand · 2 copies · chains E, P, I
- PVA · 1-amino-2-methyl-propylphosphonic acid · ligand · 2 copies · chains E, P, I
- LAC · Lactic acid · ligand · chains E, P, I
- SO4 · Sulfate ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- E–P · 351 Ų buried · 5 hydrogen bonds · protein-protein
- E–I · 234 Ų buried · 3 hydrogen bonds · protein-protein
- P–I · 161 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 1P11 · Crystal structures of alpha-lytic protease complexes with irreversibly bound phosphonate… · the same entry in another collection · chain E against E, TM-score 1.00
- P00778 · AlphaFold monomer V2.0 prediction for alpha-lytic protease (P00778) · a predicted model of the same protein · chain E 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
- Every structure of UniProt P00778
- Elsewhere: RCSB PDB 1P11 · PDBe 1P11 · UniProt P00778
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