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Structure of liver pyruvate kinase in complex with anthraquinone derivative 47

Analyse Structure of liver pyruvate kinase in complex with anthraquinone derivative 47 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QZU
Type: protein
Length: 3,412 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pkl
Ligands: FBP, OXL, I4L, MG, K
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Pkl	protein	422	48% helix, 17% strand	—
B	Pkl	protein	435	48% helix, 16% strand	—
C	Pkl	protein	425	47% helix, 17% strand	—
D, H	Pkl	protein	425	48% helix, 17% strand	—
F	Pkl	protein	435	47% helix, 16% strand	—
G	Pkl	protein	423	48% helix, 17% strand	—

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
I4L · (2~{S})-2-[2-[4-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]sulfonylpiperazin-1-yl]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid · 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	824	0.87	0.90	58	empty
2	1077	0.87	0.88	69	empty
3	347	0.87	0.96	43	empty
4	337	0.86	0.96	42	empty
5	339	0.86	0.96	43	empty

Interfaces

13 interfaces between chains.

B–D · 2669 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 2653 Å² buried · 39 hydrogen bonds · protein-protein
E–G · 2647 Å² buried · 42 hydrogen bonds · protein-protein
F–H · 2641 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 1662 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

7QZU · Structure of liver pyruvate kinase in complex with anthraqui derivative 47 · 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
Elsewhere: RCSB PDB 7QZU · PDBe 7QZU

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