MolNFT v1 · #154302 · protein

Structure of RNase J2 from staphylococcus epidermidis

6K6W · Ribonuclease J 2: “Structure of RNase J2 from staphylococcus epidermidis”. X-ray diffraction, 1 ligand (MN), 18 pockets (best druggability 0.75). MolNFT v1 #154302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6K6W
Type: protein
Length: 1,772 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease J 2
EC: 3.1.-.-
UniProt: Q8CST0
Ligands: MN
Pockets: 18 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease J 2 (EC 3.1.-.-)	protein	442	31% helix, 26% strand	Q8CST0
B, D	Ribonuclease J 2 (EC 3.1.-.-)	protein	443	32% helix, 26% strand	Q8CST0
C	Ribonuclease J 2 (EC 3.1.-.-)	protein	444	32% helix, 26% strand	Q8CST0

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	707	0.75	0.81	68	empty
2	794	0.74	0.79	65	empty
3	732	0.73	0.79	61	empty
4	728	0.72	0.78	58	empty
5	400	0.71	0.82	52	empty

Interfaces

2 interfaces between chains.

B–D · 955 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 874 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6K6W · Structure of RNase J2 from Staphylococcus epidermidis · the same entry in another collection · chain A against A, TM-score 1.00
Q8CST0 · AlphaFold monomer V2.0 prediction for ribonuclease J 2 (Q8CST0) · 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 Q8CST0
Elsewhere: RCSB PDB 6K6W · PDBe 6K6W · UniProt Q8CST0

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