Research workbench
Nucleotide-bound open form of a putative sugar kinase MK0840 from methanopyrus kandleri
Analyse Nucleotide-bound open form of a putative sugar kinase MK0840 from methanopyrus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BGA
- Type
- protein
- Length
- 1,264 residues
- Chains
- 4
- 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
- ADP, BGC, GLC, FRU, K, MG
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Predicted molecular chaperone distantly related to HSP70-F old metalloproteases | protein | 314 | 44% helix, 23% strand | Q8TX37 |
| C | Predicted molecular chaperone distantly related to HSP70-F old metalloproteases | protein | 322 | 41% helix, 23% strand | Q8TX37 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, C, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, C, D
- K · Potassium ion · metal · 8 copies · chains A, B, D, C
- MG · Magnesium ion · metal · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.77 | 0.81 | 80 | BGC, MG, ADP |
| 2 | 624 | 0.75 | 0.81 | 73 | BGC, ADP |
| 3 | 1018 | 0.73 | 0.76 | 90 | BGC, MG |
| 4 | 779 | 0.70 | 0.76 | 73 | BGC, MG, ADP |
| 5 | 183 | 0.51 | 0.78 | 25 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1527 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 798 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 98 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4BGA · Nucleotide-bound open 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 4BGA · PDBe 4BGA · UniProt Q8TX37
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