MolNFT v1 · #55008 · protein
Molecular recognition of chymotrypsin by the serine protease inhibitor ecotin from yersinia pestis
2Y6T · Chymotrypsinogen a: “Molecular recognition of chymotrypsin by the serine protease inhibitor ecotin from yersinia pestis”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.82). MolNFT v1 #55008 on GenesisL1: 3D…
- 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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