MolNFT v1 · #76721 · protein

Crystal structure of pyruvate kinase from pyrobaculum aerophilum

3QTG: “Crystal structure of pyruvate kinase from pyrobaculum aerophilum”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.74). MolNFT v1 #76721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3QTG
Type: protein
Length: 869 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase
EC: 2.7.1.40
UniProt: Q8ZYE0
Ligands: SO4
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate kinase (EC 2.7.1.40)	protein	450	38% helix, 23% strand	Q8ZYE0
B	Pyruvate kinase (EC 2.7.1.40)	protein	419	42% helix, 21% strand	Q8ZYE0

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.74	0.82	70	empty
2	538	0.73	0.82	62	empty
3	215	0.73	0.89	36	empty
4	178	0.49	0.77	31	empty
5	118	0.46	0.78	27	empty

Interfaces

1 interface between chains.

A–B · 1380 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3QTG · Crystal structure of pyruvate kinase from Pyrobaculum aerophilum · the same entry in another collection · chain A against A, TM-score 1.00
Q8ZYE0 · AlphaFold monomer V2.0 prediction for pyruvate kinase (Q8ZYE0) · 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 Q8ZYE0
Elsewhere: RCSB PDB 3QTG · PDBe 3QTG · UniProt Q8ZYE0

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