Research workbench
Crystal structure analysis of delta-chymotrypsin bound to a peptidyl chloromethyl ketone inhibitor
Analyse Crystal structure analysis of delta-chymotrypsin bound to a peptidyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DLK
- Type
- protein
- Length
- 492 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Peptidic inhibitor
- EC
- 3.4.21.1
- UniProt
- P00766
- Ligands
- PHQ, 0QE, CL
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thrombin light chain (EC 3.4.21.1) | protein | 13 | 0% helix, 0% strand | P00766 |
| B, D | Thrombin heavy chain (EC 3.4.21.1) | protein | 230 | 12% helix, 37% strand | P00766 |
| E, F | Peptidic inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 2 copies · chains B, E, D, F
- 0QE · Chloromethane · ion · 2 copies · chains B, E, D, F
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
4 interfaces between chains.
- C–D · 656 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 647 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 292 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 290 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 covalent, 2 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 1DLK · Crystal structure analysis of delta-chymotrypsin bound to a peptidyl chloromethyl ketone… · the same entry in another collection · chain F against F, TM-score 1.00
- P00766 · AlphaFold monomer V2.0 prediction for chymotrypsinogen a (P00766) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P00766
- Elsewhere: RCSB PDB 1DLK · PDBe 1DLK · UniProt P00766
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