MolNFT v1 · #125597 · protein

Crystal structure of E.COLI ligt complexed with 2'-AMP

5LDM · RNA 2',3'-cyclic phosphodiesterase: “Crystal structure of E.COLI ligt complexed with 2'-AMP”. X-ray diffraction, 2 ligands (2AM, CL), 1 pocket (best druggability 0.81). MolNFT v1 #125597 on GenesisL1: 3D structure, binding sites and…

PDB: 5LDM
Type: protein
Length: 345 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: 2AM, CL
Pockets: 1 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-)	protein	174	28% helix, 36% strand	A0A140NFI1
B	RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-)	protein	171	28% helix, 38% strand	A0A140NFI1

Ligands and binding sites

2AM · Adenosine-2'-monophosphate · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1132	0.81	0.82	90	2AM, CL

Interfaces

1 interface between chains.

A–B · 766 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5LDM · Crystal structure of E.coli LigT complexed with 2'-AMP · 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 5LDM · PDBe 5LDM · UniProt A0A140NFI1

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