Research workbench
Apo form of a putative sugar kinase MK0840 from methanopyrus kandleri (monoclinic space group)
Analyse Apo form of a putative sugar kinase MK0840 from methanopyrus kandleri… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BG8
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted molecular chaperone distantly related to HSP70-F old metalloproteases
- UniProt
- Q8TX37
- Ligands
- K, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Predicted molecular chaperone distantly related to HSP70-F old metalloproteases | protein | 314 | 43% helix, 22% strand | Q8TX37 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, 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 | 731 | 0.71 | 0.78 | 61 | empty |
| 2 | 724 | 0.71 | 0.78 | 63 | empty |
| 3 | 177 | 0.51 | 0.78 | 27 | empty |
| 4 | 171 | 0.49 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1521 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4BG8 · Apo form of a putative sugar kinase MK0840 from Methanopyrus kandleri (monoclinic space… · 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 Q8TX37
- Elsewhere: RCSB PDB 4BG8 · PDBe 4BG8 · UniProt Q8TX37
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