Research workbench

TRNA processing enzyme complex 1

Analyse TRNA processing enzyme complex 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WFQ
Type: protein + RNA
Length: 2,047 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (73-mer); Poly a polymerase
EC: 2.7.7.72
UniProt: O67911
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 58% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (73-mer)	rna	73	—	—
E	Poly a polymerase (EC 2.7.7.72)	protein	439	58% helix, 11% strand	O67911
F	Poly a polymerase (EC 2.7.7.72)	protein	436	58% helix, 11% strand	O67911
G	Poly a polymerase (EC 2.7.7.72)	protein	439	57% helix, 10% strand	O67911
H	Poly a polymerase (EC 2.7.7.72)	protein	441	58% helix, 10% strand	O67911

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.80	0.82	79	empty
2	1012	0.79	0.81	66	empty
3	995	0.78	0.80	77	empty
4	762	0.76	0.81	79	empty
5	1104	0.75	0.78	100	empty

Interfaces

9 interfaces between chains.

G–H · 1906 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1871 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 874 Å² buried · 10 hydrogen bonds · protein-nucleic
B–F · 868 Å² buried · 9 hydrogen bonds · protein-nucleic
D–H · 642 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

3WFQ · tRNA processing enzyme complex 1 · the same entry in another collection · chain H against H, TM-score 1.00
O67911 · AlphaFold monomer V2.0 prediction for cc-adding tRNA nucleotidyltransferase (O67911) · a predicted model of the same protein · chain G 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 3WFQ · PDBe 3WFQ · UniProt O67911

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