Research workbench
Murine IRGA6 bound to toxoplasma ROP5C, a pseudokinase gdi
Analyse Murine IRGA6 bound to toxoplasma ROP5C, a pseudokinase gdi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LV8
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhoptry protein 5 C; Interferon-inducible GTPase 1
- EC
- 3.6.5.-
- UniProt
- I6ZQR7, Q9QZ85
- Ligands
- ADP, GDP, MG
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhoptry protein 5 C | protein | 360 | 40% helix, 19% strand | I6ZQR7 |
| B | Interferon-inducible GTPase 1 (EC 3.6.5.-) | protein | 390 | 57% helix, 8% strand | Q9QZ85 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.75 | 0.80 | 77 | ADP, MG, EDO |
| 2 | 396 | 0.65 | 0.79 | 42 | empty |
| 3 | 180 | 0.62 | 0.84 | 30 | EDO |
| 4 | 355 | 0.60 | 0.78 | 46 | EDO |
| 5 | 109 | 0.44 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 997 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 I6ZQR7
- Every structure of UniProt Q9QZ85
- Elsewhere: RCSB PDB 4LV8 · PDBe 4LV8 · UniProt I6ZQR7 · UniProt Q9QZ85
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