MolNFT v1 · #40013 · protein

Escherichia COLI RNase II

2ID0 · Exoribonuclease 2: “Escherichia COLI RNase II”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.72). MolNFT v1 #40013 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ID0
Type: protein
Length: 2,544 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exoribonuclease 2
EC: 3.1.13.1
UniProt: P30850
Ligands: MN
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Exoribonuclease 2 (EC 3.1.13.1)	protein	636	29% helix, 29% strand	P30850

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

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	776	0.72	0.78	67	MN
2	678	0.70	0.77	65	empty
3	551	0.69	0.79	70	empty
4	901	0.69	0.75	75	empty
5	740	0.68	0.76	82	empty

Interfaces

4 interfaces between chains.

A–B · 694 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 136 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 52 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 38 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 56 modified (engineered).

Compared structures

2ID0 · Escherichia coli RNase II · the same entry in another collection · chain A against A, TM-score 1.00
P30850 · AlphaFold monomer V2.0 prediction for exoribonuclease 2 (P30850) · 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 P30850
Elsewhere: RCSB PDB 2ID0 · PDBe 2ID0 · UniProt P30850

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