MolNFT v1 · #154298 · protein

Structure of RNase J1 from staphylococcus epidermidis

6K6S · Ribonuclease J 1: “Structure of RNase J1 from staphylococcus epidermidis”. X-ray diffraction, 1 ligand (MN), 14 pockets (best druggability 0.78). MolNFT v1 #154298 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6K6S
Type: protein
Length: 884 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease J 1
EC: 3.1.-.-
UniProt: Q8CT16
Ligands: MN
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease J 1 (EC 3.1.-.-)	protein	443	26% helix, 24% strand	Q8CT16
B	Ribonuclease J 1 (EC 3.1.-.-)	protein	441	29% helix, 24% strand	Q8CT16

Ligands and binding sites

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

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

Pockets

14 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	463	0.78	0.86	70	empty
2	1089	0.77	0.79	100	empty
3	1088	0.76	0.78	108	empty
4	74	0.74	0.98	27	empty
5	104	0.73	0.94	23	empty

Interfaces

1 interface between chains.

A–B · 610 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6K6S · Structure of RNase J1 from Staphylococcus epidermidis · the same entry in another collection · chain A against A, TM-score 1.00
Q8CT16 · AlphaFold monomer V2.0 prediction for ribonuclease J 1 (Q8CT16) · a predicted model of the same protein · chain B 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 Q8CT16
Elsewhere: RCSB PDB 6K6S · PDBe 6K6S · UniProt Q8CT16

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