Research workbench
Crystal structure of porcine pancreatic trypsin with tripeptide inhibitor, tre, at pH 10
Analyse Crystal structure of porcine pancreatic trypsin with tripeptide inhibitor, tre… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XWL
- Type
- protein
- Length
- 449 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin; Acetylated-thr-arg-glu inhibitor
- EC
- 3.4.21.4
- UniProt
- P00761
- Ligands
- ACE, CA
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trypsin (EC 3.4.21.4) | protein | 223 | 10% helix, 36% strand | P00761 |
| C, D | Acetylated-thr-arg-glu inhibitor | protein | 2 | 0% helix, 0% strand | — |
| B | Trypsin (EC 3.4.21.4) | protein | 222 | 10% helix, 36% strand | P00761 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- CA · Calcium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
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 | 145 | 0.56 | 0.82 | 27 | MPD |
| 2 | 58 | 0.38 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 482 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 289 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 276 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5XWL · Crystal Structure of Porcine pancreatic trypsin with tripeptide inhibitor, TRE, at pH 10 · 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
- Every structure of UniProt P00761
- Elsewhere: RCSB PDB 5XWL · PDBe 5XWL · UniProt P00761
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