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The crystal structure of the two spectrin repeat domains from entamoeba histolytica
Analyse The crystal structure of the two spectrin repeat domains from entamoeba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NL6
- Type
- protein
- Length
- 464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calponin domain family protein
- UniProt
- N9TIJ7
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calponin domain family protein | protein | 235 | 82% helix, 0% strand | N9TIJ7 |
| B | Calponin domain family protein | protein | 229 | 80% helix, 0% strand | N9TIJ7 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.78 | 0.81 | 64 | BME |
| 2 | 470 | 0.72 | 0.82 | 51 | BME |
| 3 | 230 | 0.62 | 0.82 | 27 | empty |
| 4 | 93 | 0.49 | 0.82 | 19 | empty |
| 5 | 78 | 0.44 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1922 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 5NL6 · The crystal structure of the two spectrin repeat domains from Entamoeba histolytica · the same entry in another collection · chain A against A, TM-score 1.00
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 N9TIJ7
- Elsewhere: RCSB PDB 5NL6 · PDBe 5NL6 · UniProt N9TIJ7
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