Research workbench
Crystal structure of the free (uncomplexed) ecballium elaterium trypsin inhibitor (eeti-II)
Analyse Crystal structure of the free (uncomplexed) ecballium elaterium trypsin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W7Z
- Type
- protein
- Length
- 245 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin inhibitor II
- UniProt
- P12071
- Ligands
- NA
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Trypsin inhibitor II | protein | 31 | 10% helix, 26% strand | P12071 |
| E, G, H | Trypsin inhibitor II | protein | 30 | 10% helix, 27% strand | P12071 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 3 copies · chains B, F, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.67 | 0.79 | 50 | FMT |
| 2 | 84 | 0.37 | 0.76 | 18 | FMT |
| 3 | 77 | 0.36 | 0.77 | 20 | FMT |
Interfaces
17 interfaces between chains.
- D–H · 275 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 270 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 244 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 239 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 228 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 1W7Z · Crystal structure of the free (uncomplexed) Ecballium elaterium trypsin inhibitor… · the same entry in another collection · chain B against B, TM-score 1.00
- P12071 · AlphaFold monomer V2.0 prediction for trypsin inhibitor 2 (P12071) · a predicted model of the same protein · chain A against A, TM-score 0.88
- 2ETI · Use of restrained molecular dynamics in water to determine three- dimensional protein… · a predicted model of the same protein · chain E against A, TM-score 0.51
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 P12071
- Elsewhere: RCSB PDB 1W7Z · PDBe 1W7Z · UniProt P12071
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