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Crystal structure of RTCA.ATP.MN ternary complex

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

PDB: 3TUX
Type: protein
Length: 336 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 3'-terminal phosphate cyclase
EC: 6.5.1.4
UniProt: P46849
Ligands: ATP, MN, SO4
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4)	protein	336	34% helix, 30% strand	P46849

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
MN · Manganese (II) ion · metal · chains A
SO4 · Sulfate ion · ion · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A
GOL · Glycerol · additive · chains A

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

Pockets

5 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	93	0.77	0.98	27	EDO
2	320	0.62	0.79	44	ATP, MN, SO4
3	73	0.46	0.82	13	empty
4	92	0.45	0.80	23	empty
5	77	0.34	0.75	23	empty

Compared structures

3TUX · Crystal structure of RtcA.ATP.Mn ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
P46849 · AlphaFold monomer V2.0 prediction for RNA 3'-terminal phosphate cyclase (P46849) · a predicted model of the same protein · 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 P46849
Elsewhere: RCSB PDB 3TUX · PDBe 3TUX · UniProt P46849

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