MolNFT v1 · #12265 · protein

Pyruvate phosphate dikinase

1KBL: “Pyruvate phosphate dikinase”. X-ray diffraction, 2 ligands (SO4, NH4), 5 pockets (best druggability 0.84). MolNFT v1 #12265 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KBL
Type: protein
Length: 872 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, NH4
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate phosphate dikinase (EC 2.7.9.1)	protein	872	51% helix, 17% strand	P22983

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A
NH4 · Ammonium ion · ion · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	963	0.84	0.86	105	SO4
2	943	0.77	0.79	107	empty
3	207	0.46	0.74	38	SO4
4	75	0.39	0.78	17	empty
5	60	0.29	0.74	12	empty

Compared structures

1KBL · 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 0.99

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 1KBL · PDBe 1KBL · UniProt P22983

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