Research workbench

Cryo-EM structure of human ribonuclease P with mature tRNA

Analyse Cryo-EM structure of human ribonuclease P with mature tRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AHU
Type: protein + RNA
Length: 3,008 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H1 RNA; Ribonucleases P/MRP protein subunit POP1; Ribonuclease P protein subunit P38…
EC: 3.1.26.5
UniProt: Q99575, P78345, O95707, Q969H6, Q9BUL9, O75817, O95059, P78346, Q9H633, O75818
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 13 distinct chains · 30% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H1 RNA	rna	341	—	—
B	Ribonucleases P/MRP protein subunit POP1 (EC 3.1.26.5)	protein	774	33% helix, 16% strand	Q99575
C	Ribonuclease P protein subunit P38 (EC 3.1.26.5)	protein	182	22% helix, 15% strand	P78345
D	Ribonuclease P protein subunit P29 (EC 3.1.26.5)	protein	145	19% helix, 22% strand	O95707
E	Ribonuclease P/MRP protein subunit POP5 (EC 3.1.26.5)	protein	147	46% helix, 18% strand	Q969H6
F	Ribonuclease P protein subunit P25 (EC 3.1.26.5)	protein	129	23% helix, 32% strand	Q9BUL9
G	Ribonuclease P protein subunit P20 (EC 3.1.26.5)	protein	131	22% helix, 21% strand	O75817
H	Ribonuclease P protein subunit P14 (EC 3.1.26.5)	protein	121	24% helix, 26% strand	O95059
I	Ribonuclease P protein subunit P30 (EC 3.1.26.5)	protein	236	37% helix, 12% strand	P78346
J	Ribonuclease P protein subunit P30 (EC 3.1.26.5)	protein	247	35% helix, 14% strand	P78346
K	Ribonuclease P protein subunit P21 (EC 3.1.26.5)	protein	121	44% helix, 12% strand	Q9H633
L	Ribonuclease P protein subunit P40 (EC 3.1.26.5)	protein	362	20% helix, 33% strand	O75818
T	TRNA	rna	72	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1052	0.88	0.89	119	empty
2	528	0.84	0.91	55	empty
3	903	0.83	0.85	92	empty
4	828	0.83	0.86	64	empty
5	341	0.82	0.92	55	empty

Interfaces

35 interfaces between chains.

A–B · 6299 Å² buried · 122 hydrogen bonds · protein-nucleic
H–L · 2381 Å² buried · 20 hydrogen bonds · protein-protein
C–K · 1864 Å² buried · 13 hydrogen bonds · protein-protein
A–G · 1738 Å² buried · 28 hydrogen bonds · protein-nucleic
A–K · 1706 Å² buried · 30 hydrogen bonds · protein-nucleic

Compared structures

6AHU · Cryo-EM structure of human Ribonuclease P with mature tRNA · the same entry in another collection · chain T against T, 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 Q99575
Every structure of UniProt P78345
Every structure of UniProt O95707
Every structure of UniProt Q969H6
Every structure of UniProt Q9BUL9
Every structure of UniProt O75817
Every structure of UniProt O95059
Every structure of UniProt P78346
Every structure of UniProt Q9H633
Every structure of UniProt O75818
Elsewhere: RCSB PDB 6AHU · PDBe 6AHU · UniProt Q99575 · UniProt P78345 · UniProt O95707 · UniProt Q969H6 · UniProt Q9BUL9 · UniProt O75817 · UniProt O95059 · UniProt P78346 · UniProt Q9H633 · UniProt O75818

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