MolNFT v1 · #24957 · protein

Pyruvate phosphate dikinase from maize

1VBG · PYRUVATE,ORTHOPHOSPHATE dikinase: “Pyruvate phosphate dikinase from maize”. X-ray diffraction, 2 ligands (MG, SO4), 7 pockets (best druggability 0.74). MolNFT v1 #24957 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VBG
Type: protein
Length: 874 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PYRUVATE,ORTHOPHOSPHATE dikinase
EC: 2.7.9.1
UniProt: P11155
Ligands: MG, SO4
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PYRUVATE,ORTHOPHOSPHATE dikinase (EC 2.7.9.1)	protein	874	48% helix, 17% strand	P11155

Ligands and binding sites

MG · Magnesium ion · metal · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

7 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	934	0.74	0.78	83	SO4
2	432	0.64	0.77	50	empty
3	115	0.53	0.81	17	empty
4	116	0.46	0.78	22	empty
5	169	0.43	0.74	26	empty

Compared structures

1VBG · Pyruvate Phosphate Dikinase from Maize · the same entry in another collection · chain A against A, TM-score 1.00
P11155 · AlphaFold monomer V2.0 prediction for pyruvate, phosphate dikinase 1, chloroplastic… · a predicted model of the same protein · chain A against A, TM-score 0.76

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 P11155
Elsewhere: RCSB PDB 1VBG · PDBe 1VBG · UniProt P11155

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