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The crystal structure of the acyl transferase domain of spnd complex with benzylmalonyl

Analyse The crystal structure of the acyl transferase domain of spnd complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YDM
Type: protein
Length: 408 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pks
UniProt: A0A0E3JLZ0
Ligands: DUW
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pks	protein	408	48% helix, 14% strand	A0A0E3JLZ0

Ligands and binding sites

DUW · (2R)-2-methanoyl-3-phenyl-propanoic acid · ligand · chains A

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

Pockets

5 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	515	0.75	0.83	56	DUW
2	150	0.54	0.81	18	empty
3	86	0.46	0.80	18	empty
4	124	0.41	0.75	28	empty
5	56	0.32	0.76	16	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5YDM · The crystal structure of the Acyl Transferase domain of SpnD complex with benzylmalonyl · 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 A0A0E3JLZ0
Elsewhere: RCSB PDB 5YDM · PDBe 5YDM · UniProt A0A0E3JLZ0

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