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Crystal structure of the GDP-bound fast hydrolyzing mutant (V71A/K73Q) of EHRABX3 from entamoeba histolytica
Analyse Crystal structure of the GDP-bound fast hydrolyzing mutant (V71A/K73Q) of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C1S
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small GTPase EHRABX3
- UniProt
- Q5NT25
- Ligands
- GDP
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small GTPase EHRABX3 | protein | 288 | 30% helix, 14% strand | Q5NT25 |
| B | Small GTPase EHRABX3 | protein | 283 | 33% helix, 13% strand | Q5NT25 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.80 | 0.84 | 81 | empty |
| 2 | 1050 | 0.79 | 0.80 | 105 | empty |
| 3 | 462 | 0.68 | 0.79 | 56 | empty |
| 4 | 524 | 0.67 | 0.78 | 51 | empty |
| 5 | 161 | 0.59 | 0.83 | 30 | empty |
Modifications
Observed in the structure: 17 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 5C1S · Crystal structure of the GDP-bound fast hydrolyzing mutant (V71A/K73Q) of EhRabX3 from… · 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 Q5NT25
- Elsewhere: RCSB PDB 5C1S · PDBe 5C1S · UniProt Q5NT25
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