Research workbench
Crystal structure of peg-bound SH3 domain of myosin ib from entamoeba histolytica
Analyse Crystal structure of peg-bound SH3 domain of myosin ib from entamoeba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XG9
- Type
- protein
- Length
- 471 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin ib
- UniProt
- C4LUC7
- Ligands
- PEU, SO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D, E, G, H | Unconventional myosin ib | protein | 59 | 5% helix, 54% strand | C4LUC7 |
| F | Unconventional myosin ib | protein | 58 | 5% helix, 55% strand | C4LUC7 |
Ligands and binding sites
- PEU · 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, 59,62,65,68,71,74,77,80-heptacosaoxadooctacontan-82-ol · ligand · 2 copies · chains B, A, G
- SO4 · Sulfate ion · ion · 2 copies · chains C, D, A, F, G
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 6 copies · chains A, C, D, H, G
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.61 | 0.74 | 52 | empty |
| 2 | 389 | 0.61 | 0.76 | 33 | PG6 |
| 3 | 359 | 0.57 | 0.75 | 37 | empty |
| 4 | 79 | 0.35 | 0.76 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–F · 694 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 678 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 668 Ų buried · 14 hydrogen bonds · protein-protein
- C–H · 347 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 271 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XG9 · Crystal Structure of PEG-bound SH3 domain of Myosin IB from Entamoeba histolytica · the same entry in another collection · chain B against B, 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 5XG9 · PDBe 5XG9 · UniProt C4LUC7
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