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Catalytic domain of E. COLI RNase E in complex with 13-mer RNA

Analyse Catalytic domain of E. COLI RNase E in complex with 13-mer RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2C0B
Type: protein + RNA
Length: 498 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease E; 5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'
EC: 3.1.4.-
UniProt: P21513
Ligands: MG, ZN
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Ribonuclease E (EC 3.1.4.-)	protein	488	31% helix, 23% strand	P21513
R	5'-R(UPUPUPAPCPAPGPUPAPUPUPUP*G)-3'	rna	10	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains L
ZN · Zinc ion · metal · chains L

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1171	0.82	0.83	119	empty
2	149	0.67	0.88	30	empty
3	323	0.64	0.80	41	empty
4	121	0.45	0.78	28	empty
5	95	0.40	0.77	18	empty

Interfaces

1 interface between chains.

L–R · 1012 Å² buried · 26 hydrogen bonds · protein-nucleic

Compared structures

2C0B · Catalytic domain of E. coli RNase E in complex with 13-mer RNA · the same entry in another collection · chain L against L, TM-score 1.00
P21513 · AlphaFold monomer V2.0 prediction for ribonuclease E (P21513) · a predicted model of the same protein · chain L 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 P21513
Elsewhere: RCSB PDB 2C0B · PDBe 2C0B · UniProt P21513

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