MolNFT v1 · #86504 · protein
Crystal structure of thermococcus litoralis ADP-dependent glucokinase (gk)
4B8R: “Crystal structure of thermococcus litoralis ADP-dependent glucokinase (gk)”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.72). MolNFT v1 #86504 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4B8R
- Type
- protein
- Length
- 467 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-dependent glucokinase
- EC
- 2.7.1.147
- UniProt
- Q7M537
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-dependent glucokinase (EC 2.7.1.147) | protein | 467 | 47% helix, 20% strand | Q7M537 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A
- GOL · Glycerol · additive · 15 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.72 | 0.76 | 67 | GOL, TRS, DTT |
| 2 | 85 | 0.47 | 0.82 | 23 | PEG |
| 3 | 58 | 0.40 | 0.80 | 12 | PGE |
| 4 | 55 | 0.34 | 0.78 | 13 | empty |
| 5 | 61 | 0.33 | 0.77 | 17 | SO4 |
Compared structures
- 4B8R · Crystal Structure of Thermococcus litoralis ADP-dependent Glucokinase (GK) · the same entry in another collection · chain A against A, TM-score 1.00
- Q7M537 · AlphaFold monomer V2.0 prediction for ADP-dependent GLUCOSE/GLUCOSAMINE kinase (Q7M537) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q7M537
- Elsewhere: RCSB PDB 4B8R · PDBe 4B8R · UniProt Q7M537
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