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Crystal structure of ipp isomerase at P43212

Analyse Crystal structure of ipp isomerase at P43212 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VCG
Type: protein
Length: 1,256 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isopentenyl-diphosphate delta-isomerase
EC: 5.3.3.2
UniProt: Q746I8
Ligands: FMN
Pockets: 17 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)	protein	311	42% helix, 17% strand	Q746I8
B	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)	protein	318	44% helix, 16% strand	Q746I8
C	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)	protein	316	42% helix, 16% strand	Q746I8

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.75	0.86	48	FMN
2	366	0.75	0.86	47	FMN
3	390	0.75	0.85	50	FMN
4	378	0.74	0.85	51	FMN
5	201	0.58	0.80	22	empty

Interfaces

4 interfaces between chains.

B–C · 1177 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1166 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1151 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1149 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

1VCG · Crystal Structure of IPP isomerase at P43212 · the same entry in another collection · chain B against B, TM-score 1.00
Q746I8 · AlphaFold monomer V2.0 prediction for isopentenyl-diphosphate delta- isomerase (Q746I8) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q746I8
Elsewhere: RCSB PDB 1VCG · PDBe 1VCG · UniProt Q746I8

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