MolNFT v1 · #107204 · protein
Human mesotrypsin complexed with bikunin kunitz domain 2
4U30 · Trypsin-3: “Human mesotrypsin complexed with bikunin kunitz domain 2”. X-ray diffraction, 1 ligand (CA), 13 pockets (best druggability 0.70). MolNFT v1 #107204 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4U30
- Type
- protein
- Length
- 1,112 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin-3; Trypstatin
- EC
- 3.4.21.4
- UniProt
- P35030, P02760
- Ligands
- CA
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Trypsin-3 (EC 3.4.21.4) | protein | 224 | 11% helix, 37% strand | P35030 |
| X, Y, Z, W | Trypstatin | protein | 54 | 15% helix, 30% strand | P02760 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.70 | 0.75 | 61 | empty |
| 2 | 186 | 0.54 | 0.79 | 33 | empty |
| 3 | 268 | 0.53 | 0.75 | 33 | empty |
| 4 | 273 | 0.53 | 0.75 | 31 | empty |
| 5 | 155 | 0.52 | 0.80 | 25 | empty |
Interfaces
7 interfaces between chains.
- C–W · 635 Ų buried · 16 hydrogen bonds · protein-protein
- B–Z · 635 Ų buried · 16 hydrogen bonds · protein-protein
- A–X · 633 Ų buried · 15 hydrogen bonds · protein-protein
- D–Y · 626 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 556 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 4U30 · Human mesotrypsin complexed with bikunin Kunitz domain 2 · the same entry in another collection · chain W against W, TM-score 1.00
- P35030 · AlphaFold monomer V2.0 prediction for trypsin-3 (P35030) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P02760 · AlphaFold monomer V2.0 prediction for protein ambp (P02760) · a predicted model of the same protein · chain Y 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 P35030
- Every structure of UniProt P02760
- Elsewhere: RCSB PDB 4U30 · PDBe 4U30 · UniProt P35030 · UniProt P02760
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.