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Crystal structure of ISPH:DMAPP-complex

Analyse Crystal structure of ISPH:DMAPP-complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KEF
Type: protein
Length: 618 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
EC: 1.17.1.2
UniProt: P62623
Ligands: F3S, DMA
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2)	protein	309	42% helix, 18% strand	P62623

Ligands and binding sites

F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B
DMA · Dimethylallyl diphosphate · ligand · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	128	0.80	0.98	27	F3S, DMA
2	133	0.80	0.97	30	F3S, DMA
3	1044	0.80	0.81	71	empty
4	122	0.51	0.81	20	empty
5	66	0.51	0.86	16	empty

Interfaces

1 interface between chains.

A–B · 908 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3KEF · Crystal structure of IspH:DMAPP-complex · the same entry in another collection · chain A against A, TM-score 1.00
P62623 · AlphaFold monomer V2.0 prediction for 4-hydroxy-3-methylbut-2-enyl diphosphate reductase… · 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 P62623
Elsewhere: RCSB PDB 3KEF · PDBe 3KEF · UniProt P62623

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