MolNFT v1 · #150354 · protein
Structure of human galactokinase in complex with galactose and ADP
6GR2: “Structure of human galactokinase in complex with galactose and ADP”. X-ray diffraction, 3 ligands (ADP, GAL, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #150354 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GR2
- Type
- protein
- Length
- 3,066 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
- ADP, GAL, SO4
- 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 | 383 | 42% helix, 22% strand | P51570 |
| B | Galactokinase (EC 2.7.1.6) | protein | 382 | 43% helix, 23% strand | P51570 |
| C | Galactokinase (EC 2.7.1.6) | protein | 386 | 42% helix, 23% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 385 | 42% helix, 22% strand | P51570 |
| E | Galactokinase (EC 2.7.1.6) | protein | 384 | 43% helix, 22% strand | P51570 |
| F | Galactokinase (EC 2.7.1.6) | protein | 384 | 42% helix, 24% strand | P51570 |
| G | Galactokinase (EC 2.7.1.6) | protein | 381 | 42% helix, 23% strand | P51570 |
| H | Galactokinase (EC 2.7.1.6) | protein | 381 | 43% helix, 22% strand | P51570 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, F, 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 | 1098 | 0.80 | 0.81 | 77 | empty |
| 2 | 1193 | 0.77 | 0.79 | 102 | empty |
| 3 | 1183 | 0.77 | 0.79 | 86 | empty |
| 4 | 480 | 0.73 | 0.82 | 56 | GAL, ADP |
| 5 | 507 | 0.73 | 0.82 | 57 | GAL, ADP |
Interfaces
11 interfaces between chains.
- D–G · 836 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 759 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 689 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 623 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 231 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 6GR2 · PDBe 6GR2 · UniProt P51570
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