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Crystal structure of ADP-bound galactokinase

Analyse Crystal structure of ADP-bound galactokinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RCL
Type: protein
Length: 1,564 residues
Chains: 4
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: 17 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Galactokinase (EC 2.7.1.6)	protein	391	42% helix, 21% strand	P51570

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 11 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.81	0.83	68	empty
2	809	0.80	0.83	68	empty
3	823	0.80	0.83	71	empty
4	1165	0.79	0.81	82	empty
5	533	0.74	0.82	55	GLA, ADP, MG

Interfaces

5 interfaces between chains.

B–D · 924 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 805 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 410 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 399 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 376 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7RCL · Crystal Structure of ADP-bound Galactokinase · the same entry in another collection · chain D against D, TM-score 1.00
P51570 · AlphaFold monomer V2.0 prediction for galactokinase (P51570) · a predicted model of the same protein · chain D 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 P51570
Elsewhere: RCSB PDB 7RCL · PDBe 7RCL · UniProt P51570

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