MolNFT v1 · #139586 · protein

Crystal structure of isosesquilavandulyl diphosphate synthase from streptomyces sp. strain cnh-189 in complex with gspp and dmapp

5XK9 · Undecaprenyl diphosphate synthase: “Crystal structure of isosesquilavandulyl diphosphate synthase from streptomyces sp. strain cnh-189 in complex…”. X-ray diffraction, 3 ligands (GST, DMA, MG), 17 pockets (best druggability 0.82).…

PDB: 5XK9
Type: protein
Length: 1,698 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Undecaprenyl diphosphate synthase
UniProt: M4T4U9
Ligands: GST, DMA, MG
Pockets: 17 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Undecaprenyl diphosphate synthase	protein	214	49% helix, 14% strand	M4T4U9
B, F	Undecaprenyl diphosphate synthase	protein	209	50% helix, 15% strand	M4T4U9
C	Undecaprenyl diphosphate synthase	protein	218	48% helix, 14% strand	M4T4U9
D	Undecaprenyl diphosphate synthase	protein	209	51% helix, 15% strand	M4T4U9
G	Undecaprenyl diphosphate synthase	protein	217	48% helix, 14% strand	M4T4U9
H	Undecaprenyl diphosphate synthase	protein	208	49% helix, 15% strand	M4T4U9

Ligands and binding sites

GST · Geranyl S-thiolodiphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
DMA · Dimethylallyl diphosphate · ligand · 8 copies · chains A, B, C, E, D, F, G, H
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	168	0.82	0.97	32	MG, GST, DMA
2	174	0.81	0.96	33	MG, GST, DMA
3	172	0.81	0.96	33	MG, GST, DMA
4	938	0.78	0.80	84	MG, GST, DMA
5	229	0.78	0.91	32	MG, GST, DMA

Interfaces

12 interfaces between chains.

C–D · 1848 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 1820 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1693 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 1678 Å² buried · 25 hydrogen bonds · protein-protein
E–H · 251 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5XK9 · Crystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp.… · the same entry in another collection · 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 M4T4U9
Elsewhere: RCSB PDB 5XK9 · PDBe 5XK9 · UniProt M4T4U9

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