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Structure of liver pyruvate kinase in complex with anthraquinone derivative 1

Analyse Structure of liver pyruvate kinase in complex with anthraquinone derivative 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5SCL
Type: protein
Length: 3,405 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase
EC: 2.7.1.40
UniProt: Q16716
Ligands: FBP, OXL, AZN, MG, K
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 7 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate kinase (EC 2.7.1.40)	protein	420	47% helix, 17% strand	Q16716
B	Pyruvate kinase (EC 2.7.1.40)	protein	436	48% helix, 16% strand	Q16716
C	Pyruvate kinase (EC 2.7.1.40)	protein	424	46% helix, 17% strand	Q16716
D, H	Pyruvate kinase (EC 2.7.1.40)	protein	425	48% helix, 16% strand	Q16716
E	Pyruvate kinase (EC 2.7.1.40)	protein	419	47% helix, 17% strand	Q16716
F	Pyruvate kinase (EC 2.7.1.40)	protein	433	48% helix, 16% strand	Q16716
G	Pyruvate kinase (EC 2.7.1.40)	protein	423	47% helix, 17% strand	Q16716

Ligands and binding sites

FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 8 copies · chains A, B, C, G, D, E, F, H
OXL · Oxalate ion · ligand · 8 copies · chains A, B, C, D, E, F, G, H
AZN · Alizarin red · ligand · 6 copies · chains A, B, C, E, F, G
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
K · Potassium ion · metal · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	750	0.87	0.90	56	empty
2	363	0.86	0.95	42	empty
3	345	0.86	0.95	43	empty
4	334	0.86	0.95	42	empty
5	338	0.86	0.95	43	empty

Interfaces

13 interfaces between chains.

B–D · 2683 Å² buried · 41 hydrogen bonds · protein-protein
E–G · 2654 Å² buried · 41 hydrogen bonds · protein-protein
F–H · 2647 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 2634 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 1661 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

5SCL · Structure of liver pyruvate kinase in complex with anthraqui derivative 1 · the same entry in another collection · chain A 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 Q16716
Elsewhere: RCSB PDB 5SCL · PDBe 5SCL · UniProt Q16716

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