Research workbench
Crystal structure of trypsin in complex with lima bean trypsin inhibitor at 2.25A resolution.
Analyse Crystal structure of trypsin in complex with lima bean trypsin inhibitor at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VO7
- Type
- protein
- Length
- 502 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cationic trypsin; Bowman-birk type proteinase inhibitor
- EC
- 3.4.21.4
- UniProt
- P00760
- Ligands
- CA, NA, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cationic trypsin (EC 3.4.21.4) | protein | 223 | 10% helix, 36% strand | P00760 |
| C | Bowman-birk type proteinase inhibitor | protein | 56 | 0% helix, 32% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.67 | 0.85 | 42 | empty |
| 2 | 54 | 0.65 | 0.95 | 22 | empty |
| 3 | 156 | 0.44 | 0.75 | 27 | CL |
| 4 | 94 | 0.37 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 737 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 697 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 191 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide (disulfide).
Compared structures
- 7VO7 · Crystal structure of trypsin in complex with Lima bean trypsin inhibitor at 2.25A… · the same entry in another collection · chain C against C, TM-score 1.00
- 1TNG · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 1.00
- 1TNJ · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 1.00
- 1TNL · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 1.00
- 1TNK · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 1.00
- 1TNI · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B against A, TM-score 1.00
- 1TNH · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain B 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 P00760
- Elsewhere: RCSB PDB 7VO7 · PDBe 7VO7 · UniProt P00760
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