Research workbench
Crystal structure of TSE3-TSI3 complex with zinc ion
Analyse Crystal structure of TSE3-TSI3 complex with zinc ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N7S
- Type
- protein
- Length
- 1,042 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; Inhibitor
- UniProt
- Q9HYC5, Q9HYC4
- Ligands
- ZN, CA, NA, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein | protein | 401 | 61% helix, 2% strand | Q9HYC5 |
| B, D | Inhibitor | protein | 120 | 8% helix, 55% strand | Q9HYC4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C, D
- CL · Chloride ion · ion · 2 copies · chains A, C
- ACT · Acetate ion · additive · 17 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.77 | 0.79 | 124 | ACT, NA |
| 2 | 258 | 0.58 | 0.79 | 36 | ACT |
| 3 | 249 | 0.56 | 0.78 | 32 | empty |
| 4 | 54 | 0.51 | 0.87 | 24 | ACT |
| 5 | 56 | 0.38 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1032 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1002 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4N7S · Crystal structure of Tse3-Tsi3 complex with Zinc ion · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HYC4 · AlphaFold monomer V2.0 prediction for immune protein TSI3 (Q9HYC4) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9HYC5 · AlphaFold monomer V2.0 prediction for peptidoglycan muramidase TSE3 (Q9HYC5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9HYC5
- Every structure of UniProt Q9HYC4
- Elsewhere: RCSB PDB 4N7S · PDBe 4N7S · UniProt Q9HYC5 · UniProt Q9HYC4
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