MolNFT v1 · #120348 · protein

Structure of acryloyl-CoA lyase prpe from dinoroseobacter shibae dfl 12

5GXD · AMP-dependent synthetase and ligase: “Structure of acryloyl-CoA lyase prpe from dinoroseobacter shibae dfl 12”. X-ray diffraction, 3 ligands (AMP, AKR, COA), 3 pockets (best druggability 0.82). MolNFT v1 #120348 on GenesisL1: 3D…

PDB: 5GXD
Type: protein
Length: 627 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AMP-dependent synthetase and ligase
EC: 6.2.1.-
UniProt: A8LRC0
Ligands: AMP, AKR, COA
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AMP-dependent synthetase and ligase (EC 6.2.1.-)	protein	627	33% helix, 24% strand	A8LRC0

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A
AKR · Acrylic acid · ligand · chains A
COA · Coenzyme A · ligand · chains A
GOL · Glycerol · additive · 5 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1108	0.82	0.83	121	AMP, AKR, COA, GOL
2	95	0.39	0.77	19	empty
3	105	0.37	0.74	26	empty

Compared structures

5GXD · Structure of acryloyl-CoA lyase PrpE from Dinoroseobacter shibae DFL 12 · 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 A8LRC0
Elsewhere: RCSB PDB 5GXD · PDBe 5GXD · UniProt A8LRC0

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