Research workbench
Nucleotide-bound closed form of a putative sugar kinase MK0840 from methanopyrus kandleri
Analyse Nucleotide-bound closed form of a putative sugar kinase MK0840 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BGB
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sugar kinase MK0840
- UniProt
- Q8TX37
- Ligands
- ADP, K, MG, CA
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sugar kinase MK0840 | protein | 316 | 44% helix, 22% strand | Q8TX37 |
| B | Putative sugar kinase MK0840 | protein | 315 | 44% helix, 23% strand | Q8TX37 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.80 | 0.83 | 93 | ADP, GOL, K, MG |
| 2 | 953 | 0.76 | 0.78 | 97 | ADP, GOL, MG, CA |
| 3 | 173 | 0.53 | 0.79 | 29 | GOL |
Interfaces
1 interface between chains.
- A–B · 757 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4BGB · Nucleotide-bound closed form of a putative sugar kinase MK0840 from Methanopyrus kandleri · 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 4BGB · PDBe 4BGB · UniProt Q8TX37
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