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IPP:DMAPP isomerase type II apo structure

Analyse IPP:DMAPP isomerase type II apo structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1P0K
Type: protein
Length: 615 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isopentenyl-diphosphate delta-isomerase
EC: 5.3.3.2
UniProt: P50740
Ligands: PO4
Pockets: 7 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)	protein	306	47% helix, 17% strand	P50740
B	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)	protein	309	50% helix, 16% strand	P50740

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	151	0.55	0.81	30	empty
2	147	0.43	0.75	24	empty
3	153	0.43	0.74	24	empty
4	114	0.43	0.77	21	empty
5	173	0.42	0.74	33	PO4

Interfaces

1 interface between chains.

A–B · 519 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1P0K · IPP:DMAPP isomerase type II apo structure · the same entry in another collection · chain A against A, TM-score 1.00
P50740 · AlphaFold monomer V2.0 prediction for isopentenyl-diphosphate delta- isomerase (P50740) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P50740
Elsewhere: RCSB PDB 1P0K · PDBe 1P0K · UniProt P50740

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