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Crystal structure of E.COLI ligt complexed with ATP

Analyse Crystal structure of E.COLI ligt complexed with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LDK
Type: protein
Length: 338 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 2',3'-cyclic phosphodiesterase
EC: 3.1.4.-
UniProt: A0A140NFI1
Ligands: ATP
Pockets: 4 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-)	protein	166	26% helix, 40% strand	A0A140NFI1
B	RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-)	protein	172	27% helix, 37% strand	A0A140NFI1

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains B

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	271	0.54	0.76	28	ATP
2	233	0.51	0.75	27	empty
3	126	0.41	0.75	25	empty
4	51	0.31	0.77	10	empty

Interfaces

1 interface between chains.

A–B · 633 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5LDK · Crystal structure of E.coli LigT complexed with ATP · 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 A0A140NFI1
Elsewhere: RCSB PDB 5LDK · PDBe 5LDK · UniProt A0A140NFI1

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