MolNFT v1 · #139994 · protein
Crystal structure of porcine pancreatic trypsin with tripeptide inhibitor, tre, at pH 7
5XWJ: “Crystal structure of porcine pancreatic trypsin with tripeptide inhibitor, tre, at pH 7”. X-ray diffraction, 2 ligands (ACE, CA), 2 pockets (best druggability 0.56). MolNFT v1 #139994 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XWJ
- 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 | 164 | 0.56 | 0.81 | 28 | MPD |
| 2 | 50 | 0.36 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 465 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 285 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5XWJ · Crystal Structure of Porcine pancreatic trypsin with tripeptide inhibitor, TRE, at pH 7 · 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 5XWJ · PDBe 5XWJ · UniProt P00761
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