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Crystal structure of PKM2 R399E mutant complexed with fbp and serine

Analyse Crystal structure of PKM2 R399E mutant complexed with fbp and serine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X0I
Type: protein
Length: 2,069 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase pkm
EC: 2.7.1.40
UniProt: P14618
Ligands: FBP, SER, PYR, MG, K
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Pyruvate kinase pkm (EC 2.7.1.40)	protein	518	39% helix, 21% strand	P14618
B	Pyruvate kinase pkm (EC 2.7.1.40)	protein	515	40% helix, 21% strand	P14618

Ligands and binding sites

FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
SER · Serine · ligand · 4 copies · chains A, B, C, D
PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
K · Potassium ion · metal · 4 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	949	0.87	0.89	75	empty
2	297	0.86	0.96	41	empty
3	298	0.85	0.96	43	empty
4	549	0.79	0.86	73	PYR, MG
5	540	0.78	0.85	78	PYR, MG

Interfaces

6 interfaces between chains.

C–D · 3039 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 3039 Å² buried · 34 hydrogen bonds · protein-protein
A–C · 1321 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 1295 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 46 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5X0I · Crystal structure of PKM2 R399E mutant complexed with FBP and serine · the same entry in another collection · chain D against D, TM-score 1.00
P14618 · AlphaFold monomer V2.0 prediction for pyruvate kinase pkm (P14618) · 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 P14618
Elsewhere: RCSB PDB 5X0I · PDBe 5X0I · UniProt P14618

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