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Crystal structure of ipp isomerase at I422

Analyse Crystal structure of ipp isomerase at I422 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VCF
Type: protein
Length: 597 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: Q746I8
Ligands: FMN, CD
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)	protein	299	42% helix, 16% strand	Q746I8
B	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)	protein	298	41% helix, 16% strand	Q746I8

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
CD · Cadmium ion · metal · 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	235	0.72	0.87	38	FMN
2	201	0.72	0.88	38	FMN
3	119	0.41	0.75	23	empty
4	102	0.41	0.76	22	empty
5	74	0.38	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 110 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

1VCF · Crystal Structure of IPP isomerase at I422 · the same entry in another collection · chain A against A, 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 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 Q746I8
Elsewhere: RCSB PDB 1VCF · PDBe 1VCF · UniProt Q746I8

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