Research workbench
Ternary complex of procarboxypeptidase a, proproteinase E, and chymotrypsinogen C
Analyse Ternary complex of procarboxypeptidase a, proproteinase E, and chymotrypsinogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PYT
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Procarboxypeptidase a; Proproteinase E; Chymotrypsinogen C
- EC
- 3.4.17.1
- UniProt
- P00730, P05805
- Ligands
- ZN, CA
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Procarboxypeptidase a (EC 3.4.17.1) | protein | 94 | 40% helix, 22% strand | P00730 |
| B | Procarboxypeptidase a (EC 3.4.17.1) | protein | 309 | 38% helix, 17% strand | P00730 |
| C | Proproteinase E | protein | 248 | 8% helix, 33% strand | P05805 |
| D | Chymotrypsinogen C | protein | 251 | 7% helix, 33% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.84 | 0.85 | 105 | empty |
| 2 | 785 | 0.76 | 0.81 | 82 | empty |
| 3 | 163 | 0.55 | 0.81 | 30 | empty |
| 4 | 100 | 0.53 | 0.83 | 23 | empty |
| 5 | 59 | 0.51 | 0.86 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1266 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1130 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 655 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 445 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 1PYT · Ternary complex of procarboxypeptidase a, proproteinase E, and chymotrypsinogen C · the same entry in another collection · chain A against A, TM-score 1.00
- P00730 · AlphaFold monomer V2.0 prediction for carboxypeptidase A1 (P00730) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P05805 · AlphaFold monomer V2.0 prediction for proproteinase E (P05805) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P00730
- Every structure of UniProt P05805
- Elsewhere: RCSB PDB 1PYT · PDBe 1PYT · UniProt P00730 · UniProt P05805
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