MolNFT v1 · #101166 · protein
Crystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin) complexed to yrh-ecotin (M84Y/M85R/A86H ecotin)
4NIY · Cationic trypsin: “Crystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin) complexed to yrh-ecotin (M84Y/M85R/A86H…”. X-ray diffraction, 2 ligands (CA, ZN), 12 pockets (best druggability 0.82). MolNFT v1 #101166 on…
- PDB
- 4NIY
- Type
- protein
- Length
- 1,379 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cationic trypsin; Ecotin
- EC
- 3.4.21.4
- UniProt
- P00760, P23827
- Ligands
- CA, ZN
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cationic trypsin (EC 3.4.21.4) | protein | 216 | 11% helix, 38% strand | P00760 |
| B | Cationic trypsin (EC 3.4.21.4) | protein | 211 | 11% helix, 38% strand | P00760 |
| C | Cationic trypsin (EC 3.4.21.4) | protein | 212 | 11% helix, 38% strand | P00760 |
| D | Cationic trypsin (EC 3.4.21.4) | protein | 195 | 11% helix, 39% strand | P00760 |
| E | Ecotin | protein | 137 | 7% helix, 50% strand | P23827 |
| F | Ecotin | protein | 137 | 7% helix, 50% strand | P23827 |
| G | Ecotin | protein | 135 | 5% helix, 50% strand | P23827 |
| H | Ecotin | protein | 136 | 7% helix, 49% strand | P23827 |
Ligands and binding sites
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 | 902 | 0.82 | 0.84 | 102 | empty |
| 2 | 924 | 0.82 | 0.84 | 111 | empty |
| 3 | 321 | 0.50 | 0.73 | 33 | empty |
| 4 | 78 | 0.39 | 0.78 | 24 | empty |
| 5 | 100 | 0.38 | 0.75 | 20 | empty |
Interfaces
12 interfaces between chains.
- G–H · 1594 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1574 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 1047 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 955 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 910 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
Compared structures
- 4NIY · Crystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin) complexed to… · the same entry in another collection · chain B against B, TM-score 1.00
- 1TNI · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D against A, TM-score 0.99
- 1TNL · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D against A, TM-score 0.99
- 1TNG · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D 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 P00760
- Every structure of UniProt P23827
- Elsewhere: RCSB PDB 4NIY · PDBe 4NIY · UniProt P00760 · UniProt P23827
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