Research workbench
Crystal structure of TRYPSIN:MCOTI-II complex
Analyse Crystal structure of TRYPSIN:MCOTI-II complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GUX
- Type
- protein
- Length
- 771 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cationic trypsin; Trypsin inhibitor 2
- EC
- 3.4.21.4
- UniProt
- P00760, P82409
- Ligands
- CA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cationic trypsin (EC 3.4.21.4) | protein | 223 | 10% helix, 35% strand | P00760 |
| D, E, F | Trypsin inhibitor 2 | protein | 34 | 9% helix, 18% strand | P82409 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.74 | 0.79 | 92 | empty |
| 2 | 175 | 0.47 | 0.76 | 29 | empty |
| 3 | 140 | 0.46 | 0.77 | 31 | empty |
| 4 | 95 | 0.40 | 0.76 | 20 | empty |
| 5 | 54 | 0.38 | 0.81 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–D · 919 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 905 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 895 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 469 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
Compared structures
- 4GUX · Crystal structure of trypsin:MCoTi-II complex · the same entry in another collection · chain B against B, TM-score 1.00
- 1TNI · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 0.99
- 1TNL · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 0.99
- 1TNJ · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 0.99
- 1TNG · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 0.99
- 1TNK · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A 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
- Every structure of UniProt P82409
- Elsewhere: RCSB PDB 4GUX · PDBe 4GUX · UniProt P00760 · UniProt P82409
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