MolNFT v1 · #140530 · protein

The crystal structure of the acyl transferase domain of spnd complex with 2-(pent-4-yn-1-YL)MALONYL

5YDL · Pks: “The crystal structure of the acyl transferase domain of spnd complex with 2-(pent-4-yn-1-YL)MALONYL”. X-ray diffraction, 1 ligand (DUV), 4 pockets (best druggability 0.75). MolNFT v1 #140530 on GenesisL1: 3D structure, binding…

PDB: 5YDL
Type: protein
Length: 408 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pks
UniProt: A0A0E3JLZ0
Ligands: DUV
Pockets: 4 · 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

DUV · (2R)-2-methanoylhept-6-ynoic acid · ligand · chains A

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

Pockets

4 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	473	0.75	0.83	53	DUV
2	154	0.55	0.81	16	empty
3	132	0.43	0.76	29	empty
4	72	0.34	0.75	18	empty

Modifications

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

Compared structures

5YDL · The crystal structure of the Acyl Transferase domain of SpnD complex with… · 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 5YDL · PDBe 5YDL · UniProt A0A0E3JLZ0

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