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Crystal structure of sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form

Analyse Crystal structure of sulfolobus shibatae isopentenyl diphosphate isomerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VKJ
Type: protein
Length: 1,452 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: P61615
Ligands: FNR
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)	protein	363	50% helix, 15% strand	P61615

Ligands and binding sites

FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	542	0.75	0.83	51	FNR
2	534	0.74	0.82	48	FNR
3	564	0.74	0.82	53	FNR
4	552	0.74	0.82	53	FNR
5	538	0.66	0.77	78	empty

Interfaces

4 interfaces between chains.

A–B · 1583 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1581 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1577 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1574 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3VKJ · Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form · the same entry in another collection · chain A against A, TM-score 1.00
P61615 · AlphaFold monomer V2.0 prediction for isopentenyl-diphosphate delta- isomerase (P61615) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P61615
Elsewhere: RCSB PDB 3VKJ · PDBe 3VKJ · UniProt P61615

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