MolNFT v1 · #11127 · protein

K22A mutant of pyruvate, phosphate dikinase

1JDE: “K22A mutant of pyruvate, phosphate dikinase”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.85). MolNFT v1 #11127 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JDE
Type: protein
Length: 868 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate, phosphate dikinase
EC: 2.7.9.1
UniProt: P22983
Ligands: SO4
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate, phosphate dikinase (EC 2.7.9.1)	protein	868	45% helix, 13% strand	P22983

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

6 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	921	0.85	0.87	119	SO4
2	147	0.57	0.82	30	empty
3	244	0.53	0.76	37	empty
4	112	0.42	0.77	24	empty
5	97	0.40	0.76	21	empty

Compared structures

1JDE · K22A mutant of pyruvate, phosphate dikinase · the same entry in another collection · chain A against A, TM-score 1.00
P22983 · AlphaFold monomer V2.0 prediction for pyruvate, phosphate dikinase (P22983) · a predicted model of the same protein · chain A 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 P22983
Elsewhere: RCSB PDB 1JDE · PDBe 1JDE · UniProt P22983

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