MolNFT v1 · #156557 · protein
A divergent kinase lacking the glycine-rich loop regulates membrane ultrastructure of the toxoplasma parasitophorous vacuole
6M7Z · Bradyzoite pseudokinase 1: “A divergent kinase lacking the glycine-rich loop regulates membrane ultrastructure of the toxoplasma…”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.74). MolNFT v1 #156557 on…
- PDB
- 6M7Z
- Type
- protein
- Length
- 1,565 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bradyzoite pseudokinase 1
- EC
- 2.7.99.1
- Ligands
- CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bradyzoite pseudokinase 1 (EC 2.7.99.1) | protein | 262 | 48% helix, 14% strand | — |
| B | Bradyzoite pseudokinase 1 (EC 2.7.99.1) | protein | 258 | 49% helix, 14% strand | — |
| C | Bradyzoite pseudokinase 1 (EC 2.7.99.1) | protein | 262 | 48% helix, 14% strand | — |
| D | Bradyzoite pseudokinase 1 (EC 2.7.99.1) | protein | 255 | 48% helix, 15% strand | — |
| E | Bradyzoite pseudokinase 1 (EC 2.7.99.1) | protein | 269 | 47% helix, 14% strand | — |
| F | Bradyzoite pseudokinase 1 (EC 2.7.99.1) | protein | 259 | 49% helix, 14% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains C, E
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.74 | 0.77 | 51 | empty |
| 2 | 583 | 0.74 | 0.81 | 43 | empty |
| 3 | 761 | 0.73 | 0.78 | 53 | empty |
| 4 | 600 | 0.72 | 0.80 | 62 | empty |
| 5 | 746 | 0.70 | 0.77 | 65 | empty |
Interfaces
12 interfaces between chains.
- B–E · 692 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 641 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 609 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 602 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6M7Z · A divergent kinase lacking the glycine-rich loop regulates membrane ultrastructure of the… · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 6M7Z · PDBe 6M7Z
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