MolNFT v1 · #149631 · protein + RNA

RNase E in complex with srna rrpa

6G63 · Ribonuclease E: “RNase E in complex with srna rrpa”. X-ray diffraction, 2 ligands (U, ZN), 20 pockets (best druggability 0.82). MolNFT v1 #149631 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6G63
Type: protein + RNA
Length: 1,997 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease E; RNA (5'- R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*U…
EC: 3.1.26.12
UniProt: P21513
Ligands: U, ZN
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 5 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease E (EC 3.1.26.12)	protein	494	35% helix, 25% strand	P21513
G	Ribonuclease E (EC 3.1.26.12)	protein	493	33% helix, 26% strand	P21513
L	Ribonuclease E (EC 3.1.26.12)	protein	493	33% helix, 28% strand	P21513
N	Ribonuclease E (EC 3.1.26.12)	protein	494	33% helix, 28% strand	P21513
B	RNA (5'- R(PAPAPAPAPAPAPAPAPAPAPAPAPUPUPUPUPUPUPUPUPUPUP *U)-3')	rna	23	—	—

Ligands and binding sites

U · Uridine-5'-monophosphate · ligand · chains N
ZN · Zinc ion · metal · 2 copies · chains A, G, L, N

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	759	0.82	0.86	95	U
2	764	0.81	0.85	85	empty
3	584	0.80	0.86	70	empty
4	688	0.79	0.84	71	empty
5	797	0.75	0.79	92	empty

Interfaces

6 interfaces between chains.

A–G · 3780 Å² buried · 58 hydrogen bonds · protein-protein
L–N · 3572 Å² buried · 58 hydrogen bonds · protein-protein
A–L · 1012 Å² buried · 29 hydrogen bonds · protein-protein
G–N · 992 Å² buried · 25 hydrogen bonds · protein-protein
G–B · 340 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

6G63 · RNase E in complex with sRNA RrpA · the same entry in another collection · chain B against B, 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 0.95

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 6G63 · PDBe 6G63 · UniProt P21513

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