MolNFT v1 · #149979 · protein

Crystal structure of M2 pyk in complex with alanine.

6GG3 · Pyruvate kinase pkm: “Crystal structure of M2 pyk in complex with alanine.”. X-ray diffraction, 2 ligands (ALA, PO4), 20 pockets (best druggability 0.86). MolNFT v1 #149979 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6GG3
Type: protein
Length: 6,002 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase pkm
EC: 2.7.1.40
UniProt: P14618
Ligands: ALA, PO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 8 distinct chains · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate kinase pkm (EC 2.7.1.40)	protein	519	38% helix, 20% strand	P14618
B, F, G, L	Pyruvate kinase pkm (EC 2.7.1.40)	protein	524	37% helix, 20% strand	P14618
C	Pyruvate kinase pkm (EC 2.7.1.40)	protein	521	38% helix, 20% strand	P14618
D	Pyruvate kinase pkm (EC 2.7.1.40)	protein	513	38% helix, 19% strand	P14618
E	Pyruvate kinase pkm (EC 2.7.1.40)	protein	481	39% helix, 18% strand	P14618
H	Pyruvate kinase pkm (EC 2.7.1.40)	protein	520	38% helix, 20% strand	P14618
I, J	Pyruvate kinase pkm (EC 2.7.1.40)	protein	418	45% helix, 15% strand	P14618
K	Pyruvate kinase pkm (EC 2.7.1.40)	protein	516	38% helix, 21% strand	P14618

Ligands and binding sites

ALA · Alanine · ligand · 11 copies · chains A, C, D, E, F, G, H, I, J, K, L
PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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	342	0.86	0.95	41	empty
2	346	0.86	0.95	40	empty
3	339	0.86	0.95	38	empty
4	352	0.85	0.95	42	empty
5	328	0.85	0.95	40	empty

Interfaces

23 interfaces between chains.

A–B · 2668 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2650 Å² buried · 26 hydrogen bonds · protein-protein
K–L · 2579 Å² buried · 28 hydrogen bonds · protein-protein
I–J · 2569 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2544 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6GG3 · Crystal structure of M2 PYK in complex with Alanine. · the same entry in another collection · chain L against L, 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 6GG3 · PDBe 6GG3 · UniProt P14618

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