MolNFT v1 · #186400 · protein
Crystal structure of ADP-bound galactokinase
7RCM: “Crystal structure of ADP-bound galactokinase”. X-ray diffraction, 5 ligands (ADP, GLA, MG), 5 pockets (best druggability 0.81). MolNFT v1 #186400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RCM
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- EC
- 2.7.1.6
- UniProt
- P51570
- Ligands
- ADP, GLA, MG, NA, PO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Galactokinase (EC 2.7.1.6) | protein | 391 | 42% helix, 23% strand | P51570 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.81 | 0.83 | 69 | empty |
| 2 | 389 | 0.75 | 0.86 | 48 | ADP, GLA, MG |
| 3 | 427 | 0.72 | 0.83 | 54 | ADP, GLA, MG |
| 4 | 132 | 0.49 | 0.79 | 26 | empty |
| 5 | 94 | 0.33 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 879 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 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 7RCM · PDBe 7RCM · UniProt P51570
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