Research workbench
Structural consequences of accommodation of four non-cognate amino- acid residues in the S1 pocket of bovine trypsin and chymotrypsin
Analyse Structural consequences of accommodation of four non-cognate amino- acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P2M
- Type
- protein
- Length
- 592 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chymotrypsinogen a; Pancreatic trypsin inhibitor
- EC
- 3.4.21.1
- UniProt
- P00766, P00974
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Chymotrypsinogen a (EC 3.4.21.1) | protein | 238 | 12% helix, 35% strand | P00766 |
| B, D | Pancreatic trypsin inhibitor | protein | 58 | 21% helix, 28% strand | P00974 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.71 | 0.95 | 34 | empty |
| 2 | 637 | 0.67 | 0.76 | 65 | SO4 |
| 3 | 168 | 0.61 | 0.84 | 46 | empty |
| 4 | 177 | 0.55 | 0.80 | 30 | empty |
| 5 | 172 | 0.54 | 0.80 | 30 | empty |
Interfaces
5 interfaces between chains.
- C–D · 666 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 661 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 442 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 339 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 315 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1P2M · Structural consequences of accommodation of four non-cognate amino-acid residues in the… · the same entry in another collection · chain D against D, TM-score 1.00
- P00766 · AlphaFold monomer V2.0 prediction for chymotrypsinogen a (P00766) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P00974 · AlphaFold monomer V2.0 prediction for pancreatic trypsin inhibitor (P00974) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P00766
- Every structure of UniProt P00974
- Elsewhere: RCSB PDB 1P2M · PDBe 1P2M · UniProt P00766 · UniProt P00974
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