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Crystal structure of M2 pyk in complex with serine.

Analyse Crystal structure of M2 pyk in complex with serine. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GG6
Type: protein
Length: 4,080 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase pkm
EC: 2.7.1.40
UniProt: P14618
Ligands: SER, K, MG, PO4
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Pyruvate kinase pkm (EC 2.7.1.40)	protein	510	39% helix, 21% strand	P14618

Ligands and binding sites

SER · Serine · ligand · 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
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
PO4 · Phosphate ion · ion · 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	362	0.87	0.96	52	empty
2	353	0.87	0.96	45	empty
3	365	0.87	0.96	45	empty
4	335	0.87	0.96	43	empty
5	370	0.84	0.93	36	empty

Interfaces

13 interfaces between chains.

E–F · 3102 Å² buried · 38 hydrogen bonds · protein-protein
G–H · 3079 Å² buried · 40 hydrogen bonds · protein-protein
C–D · 3056 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 3054 Å² buried · 38 hydrogen bonds · protein-protein
E–G · 1392 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (oxidation).

Compared structures

6GG6 · Crystal structure of M2 PYK in complex with Serine. · the same entry in another collection · chain C against C, TM-score 1.00
P14618 · AlphaFold monomer V2.0 prediction for pyruvate kinase pkm (P14618) · a predicted model of the same protein · chain G 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 6GG6 · PDBe 6GG6 · UniProt P14618

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