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Crystal structure of RTCA.AMP product complex

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

PDB: 3TV1
Type: protein
Length: 672 residues
Chains: 2
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: AMP, SO4, CL
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4)	protein	336	34% helix, 32% strand	P46849

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
CL · Chloride ion · ion · chains B
EDO · 1,2-ethanediol · additive · chains A
GOL · Glycerol · additive · chains A
PEG · Di(hydroxyethyl)ether · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	851	0.79	0.82	124	AMP, SO4, EDO, CL, PEG
2	82	0.76	0.98	23	empty
3	80	0.75	0.98	25	empty
4	95	0.37	0.75	20	empty
5	58	0.29	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 443 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3TV1 · Crystal structure of RtcA.AMP product 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 0.98

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 3TV1 · PDBe 3TV1 · UniProt P46849

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