MolNFT v1 · #171751 · protein
Structure of human galactokinase in complex with galactose and 2'- (BENZO[D]OXAZOL-2-ylamino)-7',8'-dihydro-1'H-SPIRO[CYCLOPENTANE-1,4'- quinazolin]-5'(6'H)-one
6ZFH: “Structure of human galactokinase in complex with galactose and 2'…”. X-ray diffraction, 2 ligands (QV2, GAL), 20 pockets (best druggability 0.80). MolNFT v1 #171751 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZFH
- Type
- protein
- Length
- 3,074 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- EC
- 2.7.1.6
- UniProt
- P51570
- Ligands
- QV2, GAL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase (EC 2.7.1.6) | protein | 386 | 42% helix, 22% strand | P51570 |
| B | Galactokinase (EC 2.7.1.6) | protein | 386 | 42% helix, 23% strand | P51570 |
| C | Galactokinase (EC 2.7.1.6) | protein | 388 | 42% helix, 22% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 385 | 42% helix, 23% strand | P51570 |
| E | Galactokinase (EC 2.7.1.6) | protein | 386 | 42% helix, 23% strand | P51570 |
| F | Galactokinase (EC 2.7.1.6) | protein | 384 | 42% helix, 23% strand | P51570 |
| G | Galactokinase (EC 2.7.1.6) | protein | 383 | 43% helix, 22% strand | P51570 |
| H | Galactokinase (EC 2.7.1.6) | protein | 376 | 43% helix, 23% strand | P51570 |
Ligands and binding sites
- QV2 · 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclopentane]-5-one · ligand · 7 copies · chains A, B, C, D, E, F, G
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.80 | 0.83 | 62 | empty |
| 2 | 989 | 0.78 | 0.80 | 90 | empty |
| 3 | 447 | 0.75 | 0.84 | 56 | GAL, QV2 |
| 4 | 393 | 0.74 | 0.84 | 52 | GAL, QV2 |
| 5 | 377 | 0.73 | 0.84 | 56 | GAL, QV2 |
Interfaces
11 interfaces between chains.
- A–C · 835 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 700 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 596 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 345 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 261 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 P51570
- Elsewhere: RCSB PDB 6ZFH · PDBe 6ZFH · UniProt P51570
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.