Research workbench
Crystal structure C-terminal SH3 domain of myosin ib from entamoeba histolytica
Analyse Crystal structure C-terminal SH3 domain of myosin ib from entamoeba histolytica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XGG
- Type
- protein
- Length
- 380 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin ib
- UniProt
- C4LUC7
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Unconventional myosin ib | protein | 64 | 5% helix, 47% strand | C4LUC7 |
| E | Unconventional myosin ib | protein | 65 | 5% helix, 46% strand | C4LUC7 |
| F | Unconventional myosin ib | protein | 59 | 5% helix, 53% strand | C4LUC7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.61 | 0.76 | 47 | empty |
| 2 | 372 | 0.55 | 0.74 | 48 | empty |
| 3 | 51 | 0.25 | 0.73 | 10 | empty |
Interfaces
8 interfaces between chains.
- B–D · 572 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 414 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 242 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 238 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5XGG · Crystal Structure C-terminal SH3 domain of Myosin IB 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 C4LUC7
- Elsewhere: RCSB PDB 5XGG · PDBe 5XGG · UniProt C4LUC7
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