Research workbench

Crystal structure of M2 pyk in complex with tryptophan.

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

PDB: 6GG5
Type: protein
Length: 1,838 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: TRP, K, PO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pyruvate kinase pkm (EC 2.7.1.40)	protein	509	39% helix, 21% strand	P14618
C, D	Pyruvate kinase pkm (EC 2.7.1.40)	protein	410	47% helix, 16% strand	P14618

Ligands and binding sites

TRP · Tryptophan · ligand · 4 copies · chains A, B, C, D
K · Potassium ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 8 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	359	0.86	0.95	43	empty
2	330	0.86	0.95	38	empty
3	910	0.76	0.79	91	PO4, K
4	564	0.76	0.83	64	PO4, K
5	759	0.75	0.80	97	TRP

Interfaces

4 interfaces between chains.

A–D · 2614 Å² buried · 35 hydrogen bonds · protein-protein
B–C · 2600 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 1138 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 1107 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

6GG5 · Crystal structure of M2 PYK in complex with Tryptophan. · 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 B against A, TM-score 0.98

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 6GG5 · PDBe 6GG5 · UniProt P14618

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.