Research workbench
Molecular recognition of chymotrypsin by the serine protease inhibitor ecotin from yersinia pestis
Analyse Molecular recognition of chymotrypsin by the serine protease inhibitor ecotin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y6T
- Type
- protein
- Length
- 1,517 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chymotrypsinogen a; Ecotin
- EC
- 3.4.21.1
- UniProt
- P00766, B1JSA0
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chymotrypsinogen a (EC 3.4.21.1) | protein | 239 | 10% helix, 36% strand | P00766 |
| E | Ecotin | protein | 141 | 4% helix, 47% strand | B1JSA0 |
| F | Ecotin | protein | 142 | 4% helix, 44% strand | B1JSA0 |
| G | Ecotin | protein | 140 | 7% helix, 46% strand | B1JSA0 |
| H | Ecotin | protein | 138 | 0% helix, 48% strand | B1JSA0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, F, B, E, C, H, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.82 | 0.83 | 122 | SO4 |
| 2 | 1120 | 0.82 | 0.83 | 122 | SO4 |
| 3 | 826 | 0.77 | 0.80 | 83 | empty |
| 4 | 152 | 0.45 | 0.76 | 26 | empty |
| 5 | 190 | 0.44 | 0.74 | 39 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1647 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1578 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 1022 Ų buried · 21 hydrogen bonds · protein-protein
- C–G · 1016 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1002 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 2Y6T · Molecular Recognition of Chymotrypsin by the Serine Protease Inhibitor Ecotin from… · the same entry in another collection · chain H against H, 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
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 B1JSA0
- Elsewhere: RCSB PDB 2Y6T · PDBe 2Y6T · UniProt P00766 · UniProt B1JSA0
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