MolNFT v1 · #51951 · protein

Crystal structure of E. COLI RNase E apoprotein - catalytic domain

2VMK · Ribonuclease E: “Crystal structure of E. COLI RNase E apoprotein - catalytic domain”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #51951 on GenesisL1: 3D structure, binding sites and…

PDB: 2VMK
Type: protein
Length: 1,930 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease E
EC: 3.1.4.-
UniProt: P21513
Ligands: ZN, SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease E (EC 3.1.4.-)	protein	489	34% helix, 28% strand	P21513
B	Ribonuclease E (EC 3.1.4.-)	protein	495	33% helix, 27% strand	P21513
C	Ribonuclease E (EC 3.1.4.-)	protein	474	32% helix, 27% strand	P21513
D	Ribonuclease E (EC 3.1.4.-)	protein	472	33% helix, 26% strand	P21513

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 3 copies · chains A, B, C

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

Pockets

20 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	1183	0.82	0.83	123	empty
2	818	0.72	0.77	83	empty
3	668	0.71	0.78	72	empty
4	389	0.70	0.82	45	empty
5	252	0.60	0.80	31	empty

Interfaces

6 interfaces between chains.

A–B · 2902 Å² buried · 41 hydrogen bonds · protein-protein
C–D · 2661 Å² buried · 38 hydrogen bonds · protein-protein
B–C · 930 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 921 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 140 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2VMK · Crystal Structure of E. coli RNase E Apoprotein - Catalytic Domain · the same entry in another collection · chain D against D, TM-score 1.00
P21513 · AlphaFold monomer V2.0 prediction for ribonuclease E (P21513) · a predicted model of the same protein · chain A against A, TM-score 0.68

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 2VMK · PDBe 2VMK · UniProt P21513

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