Research workbench

TRNA processing enzyme complex 3

Analyse TRNA processing enzyme complex 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WFS
Type: protein + RNA
Length: 1,029 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (74-mer); Poly a polymerase
EC: 2.7.7.72
UniProt: O67911
Ligands: SO4
Pockets: 13 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 57% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (74-mer)	rna	74	—	—
C	Poly a polymerase (EC 2.7.7.72)	protein	436	57% helix, 11% strand	O67911
D	Poly a polymerase (EC 2.7.7.72)	protein	445	56% helix, 11% strand	O67911

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	883	0.79	0.82	77	empty
2	585	0.78	0.84	52	SO4
3	660	0.77	0.83	47	SO4
4	817	0.75	0.80	58	empty
5	860	0.70	0.77	39	empty

Interfaces

5 interfaces between chains.

B–D · 1204 Å² buried · 28 hydrogen bonds · protein-nucleic
A–C · 1116 Å² buried · 27 hydrogen bonds · protein-nucleic
C–D · 472 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 247 Å² buried · 1 hydrogen bond · protein-nucleic
B–C · 121 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

3WFS · tRNA processing enzyme complex 3 · the same entry in another collection · chain A against A, TM-score 1.00
O67911 · AlphaFold monomer V2.0 prediction for cc-adding tRNA nucleotidyltransferase (O67911) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 O67911
Elsewhere: RCSB PDB 3WFS · PDBe 3WFS · UniProt O67911

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.