MolNFT v1 · #140531 · protein

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

5YDM · Pks: “The crystal structure of the acyl transferase domain of spnd complex with benzylmalonyl”. X-ray diffraction, 1 ligand (DUW), 5 pockets (best druggability 0.75). MolNFT v1 #140531 on GenesisL1: 3D structure, binding sites and…

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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