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Crystal structure of tomato methylketone synthase I complexed with methyl-3-hydroxydodecanoate

Analyse Crystal structure of tomato methylketone synthase I complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3STU
Type: protein
Length: 517 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylketone synthase 1
UniProt: E0YCS2
Ligands: DKA, DK3
Pockets: 3 · best druggability 0.76

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methylketone synthase 1	protein	258	43% helix, 16% strand	E0YCS2
B	Methylketone synthase 1	protein	259	41% helix, 17% strand	E0YCS2

Ligands and binding sites

DKA · Decanoic acid · ligand · chains A
DK3 · methyl (3S)-3-hydroxydodecanoate · ligand · chains B

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

Pockets

3 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	240	0.76	0.89	34	DK3
2	347	0.74	0.85	53	DKA
3	101	0.36	0.74	24	empty

Interfaces

1 interface between chains.

A–B · 893 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3STU · Crystal Structure of tomato Methylketone Synthase I complexed with… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt E0YCS2
Elsewhere: RCSB PDB 3STU · PDBe 3STU · UniProt E0YCS2

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