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Crystal structure of IdnL7

Analyse Crystal structure of IdnL7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AKD
Type: protein
Length: 488 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.1
Source: Streptomyces sp. ML694-90F3
Molecule: AMP-dependent synthetase and ligase
UniProt: A0A077KUW8
Ligands: A5A
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · resolution 2.1 · 1 distinct chain · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AMP-dependent synthetase and ligase	protein	488	34% helix, 26% strand	A0A077KUW8

Ligands and binding sites

A5A · 5'-O-(N-(L-alanyl)-sulfamoyl)adenosine · ligand · chains A
GOL · Glycerol · additive · 2 copies · 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	690	0.78	0.83	69	A5A, GOL
2	95	0.53	0.83	17	GOL
3	74	0.33	0.75	18	empty
4	67	0.33	0.76	15	empty

Compared structures

6AKD · Crystal structure of IDNL7 · 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 A0A077KUW8
Elsewhere: RCSB PDB 6AKD · PDBe 6AKD · UniProt A0A077KUW8

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