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Crystal structure of a synthase from streptomyces sp. CL190 with dmaspp

Analyse Crystal structure of a synthase from streptomyces sp. CL190 with dmaspp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YGK
Type: protein
Length: 1,683 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclolavandulyl diphosphate synthase
UniProt: X5IYJ5
Ligands: DST, MG
Pockets: 15 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclolavandulyl diphosphate synthase	protein	210	50% helix, 17% strand	X5IYJ5
B, D, E	Cyclolavandulyl diphosphate synthase	protein	208	49% helix, 17% strand	X5IYJ5
C	Cyclolavandulyl diphosphate synthase	protein	217	49% helix, 15% strand	X5IYJ5
F, G	Cyclolavandulyl diphosphate synthase	protein	208	49% helix, 15% strand	X5IYJ5
H	Cyclolavandulyl diphosphate synthase	protein	216	48% helix, 15% strand	X5IYJ5

Ligands and binding sites

DST · Dimethylallyl S-thiolodiphosphate · ligand · 16 copies · chains A, B, F, C, H, D, G, E
MG · Magnesium ion · metal · 8 copies · chains A, B, C, H, D, E, F, G

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	207	0.81	0.94	31	DST, MG
2	367	0.64	0.79	43	DST, MG
3	243	0.62	0.81	37	DST, MG
4	237	0.60	0.80	29	DST, MG
5	204	0.60	0.81	24	DST, MG

Interfaces

10 interfaces between chains.

C–H · 1859 Å² buried · 27 hydrogen bonds · protein-protein
B–F · 1449 Å² buried · 23 hydrogen bonds · protein-protein
D–G · 1398 Å² buried · 21 hydrogen bonds · protein-protein
A–E · 1368 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 365 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5YGK · Crystal structure of a synthase from Streptomyces sp. CL190 with dmaspp · the same entry in another collection · chain D against D, 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 X5IYJ5
Elsewhere: RCSB PDB 5YGK · PDBe 5YGK · UniProt X5IYJ5

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