Research workbench

Crystal structure of RNase III complexed with double-stranded RNA and cmp (type II cleavage)

Analyse Crystal structure of RNase III complexed with double-stranded RNA and cmp (type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4M2Z
Type: protein + RNA
Length: 492 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease 3; RNA10
EC: 3.1.26.3
UniProt: O67082
Ligands: C, MG
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 59% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease 3 (EC 3.1.26.3)	protein	220	60% helix, 10% strand	O67082
B	Ribonuclease 3 (EC 3.1.26.3)	protein	218	58% helix, 11% strand	O67082
C, D	RNA10	rna	27	—	—

Ligands and binding sites

C · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 6 copies · chains A, D, B, C

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

Pockets

4 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	1020	0.79	0.82	71	MG, C
2	1018	0.79	0.81	74	MG, C
3	63	0.65	0.94	16	empty
4	53	0.28	0.75	14	empty

Interfaces

6 interfaces between chains.

A–B · 1313 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 867 Å² buried · 26 hydrogen bonds · protein-nucleic
B–C · 843 Å² buried · 23 hydrogen bonds · protein-nucleic
A–C · 700 Å² buried · 17 hydrogen bonds · protein-nucleic
B–D · 674 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

4M2Z · Crystal structure of RNASE III complexed with double-stranded RNA and CMP (TYPE II… · the same entry in another collection · chain C against C, TM-score 1.00
O67082 · AlphaFold monomer V2.0 prediction for ribonuclease 3 (O67082) · a predicted model of the same protein · chain B 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 O67082
Elsewhere: RCSB PDB 4M2Z · PDBe 4M2Z · UniProt O67082

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.