MolNFT v1 · #119879 · protein
Succinic acid bound trypsin crystallized as dimer
5GIB · Cationic trypsin: “Succinic acid bound trypsin crystallized as dimer”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.51). MolNFT v1 #119879 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GIB
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cationic trypsin
- EC
- 3.4.21.4
- UniProt
- P00760
- Ligands
- CA
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cationic trypsin (EC 3.4.21.4) | protein | 218 | 11% helix, 34% strand | P00760 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.51 | 0.83 | 30 | empty |
| 2 | 216 | 0.50 | 0.76 | 31 | empty |
| 3 | 56 | 0.41 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 420 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5GIB · Succinic acid bound trypsin crystallized as dimer · the same entry in another collection · chain B against B, TM-score 1.00
- 1TNG · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 0.99
- 1TNL · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 0.99
- 1TNI · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 0.99
- 1TNH · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 0.99
- 1TNK · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 0.99
- 1TNJ · Prediction of novel serine protease inhibitors · 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 P00760
- Elsewhere: RCSB PDB 5GIB · PDBe 5GIB · UniProt P00760
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