MolNFT v1 · #65768 · protein

Activator-bound structure of human pyruvate kinase M2

3H6O · Pyruvate kinase isozymes M1/M2: “Activator-bound structure of human pyruvate kinase M2”. X-ray diffraction, 3 ligands (FBP, D8G, UNX), 20 pockets (best druggability 0.87). MolNFT v1 #65768 on GenesisL1: 3D structure, binding sites…

PDB: 3H6O
Type: protein
Length: 1,978 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase isozymes M1/M2
EC: 2.7.1.40
UniProt: P14618
Ligands: FBP, D8G, UNX
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40)	protein	490	41% helix, 20% strand	P14618
B	Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40)	protein	513	39% helix, 21% strand	P14618
C	Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40)	protein	468	43% helix, 16% strand	P14618
D	Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40)	protein	507	39% helix, 20% strand	P14618

Ligands and binding sites

FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
D8G · 6-(2-fluorobenzyl)-2,4-dimethyl-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one · ligand · 2 copies · chains A, B, C, D
UNX · Unknown atom or ion · ion · 31 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	366	0.87	0.96	44	D8G, UNX
2	374	0.86	0.95	43	D8G
3	674	0.85	0.90	69	empty
4	141	0.75	0.93	19	empty
5	253	0.72	0.87	38	empty

Interfaces

6 interfaces between chains.

C–D · 2665 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 2610 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 1475 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1420 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 43 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3H6O · Activator-Bound Structure of Human Pyruvate Kinase M2 · 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 P14618
Elsewhere: RCSB PDB 3H6O · PDBe 3H6O · UniProt P14618

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