MolNFT v1 · #168146 · protein + RNA

Structure of yeast RNase mrp holoenzyme

6W6V · RNA component of RNase mrp NME1: “Structure of yeast RNase mrp holoenzyme”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #168146 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6W6V
Type: protein + RNA
Length: 2,600 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA component of RNase mrp NME1; Ribonucleases P/MRP protein subunit POP1; Rnases MRP/P…
EC: 3.1.26.5
UniProt: P41812, P38336, P28005, P53218, P38291, P38208, P38786, P40993, Q12530
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 11 distinct chains · 31% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA component of RNase mrp NME1	rna	294	—	—
B	Ribonucleases P/MRP protein subunit POP1 (EC 3.1.26.5)	protein	780	28% helix, 15% strand	P41812
D	Rnases MRP/P 32.9 kda subunit	protein	212	27% helix, 18% strand	P38336
E	Ribonuclease P/MRP protein subunit POP5 (EC 3.1.26.5)	protein	169	37% helix, 15% strand	P28005
F	Ribonucleases P/MRP protein subunit POP6 (EC 3.1.26.5)	protein	158	27% helix, 27% strand	P53218
G	Ribonucleases P/MRP protein subunit POP7 (EC 3.1.26.5)	protein	126	21% helix, 33% strand	P38291
H	Ribonucleases P/MRP protein subunit POP8 (EC 3.1.26.5)	protein	125	22% helix, 15% strand	P38208
I	Ribonuclease P/MRP protein subunit RPP1 (EC 3.1.26.5)	protein	243	34% helix, 13% strand	P38786
J	Ribonuclease P/MRP protein subunit RPP1 (EC 3.1.26.5)	protein	293	33% helix, 15% strand	P38786
K	Ribonuclease mrp protein subunit SNM1	protein	79	33% helix, 0% strand	P40993
L	Ribonuclease mrp protein subunit RMP1	protein	121	61% helix, 0% strand	Q12530

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	760	0.86	0.90	71	empty
2	1012	0.85	0.87	77	empty
3	677	0.85	0.89	85	empty
4	1006	0.84	0.86	97	empty
5	951	0.82	0.84	82	empty

Interfaces

24 interfaces between chains.

A–B · 7279 Å² buried · 112 hydrogen bonds · protein-nucleic
D–J · 2347 Å² buried · 19 hydrogen bonds · protein-protein
A–G · 1902 Å² buried · 29 hydrogen bonds · protein-nucleic
D–K · 1785 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1498 Å² buried · 18 hydrogen bonds · protein-nucleic

Compared structures

6W6V · Structure of yeast RNase MRP holoenzyme · the same entry in another collection · chain L against L, TM-score 1.00
P38786 · AlphaFold monomer V2.0 prediction for ribonuclease P/MRP protein subunit RPP1 (P38786) · a predicted model of the same protein · chain I against A, TM-score 0.96

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 P41812
Every structure of UniProt P38336
Every structure of UniProt P28005
Every structure of UniProt P53218
Every structure of UniProt P38291
Every structure of UniProt P38208
Every structure of UniProt P38786
Every structure of UniProt P40993
Every structure of UniProt Q12530
Elsewhere: RCSB PDB 6W6V · PDBe 6W6V · UniProt P41812 · UniProt P38336 · UniProt P28005 · UniProt P53218 · UniProt P38291 · UniProt P38208 · UniProt P38786 · UniProt P40993 · UniProt Q12530

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