MolNFT v1 · #99422 · protein + RNA

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

4M30 · Ribonuclease 3: “Crystal structure of RNase III complexed with double-stranded RNA and AMP (type II cleavage)”. X-ray diffraction, 2 ligands (A, MG), 7 pockets (best druggability 0.83). MolNFT v1 #99422 on GenesisL1: 3D structure…

PDB: 4M30
Type: protein + RNA
Length: 492 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease 3; RNA12
EC: 3.1.26.3
UniProt: O67082
Ligands: A, MG
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 60% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease 3 (EC 3.1.26.3)	protein	220	60% helix, 11% strand	O67082
B	Ribonuclease 3 (EC 3.1.26.3)	protein	218	61% helix, 11% strand	O67082
C, D	RNA12	rna	27	—	—

Ligands and binding sites

A · Adenosine-5'-monophosphate · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 9 copies · chains A, D, B, C
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B

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

Pockets

7 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	557	0.83	0.89	65	MG, A
2	151	0.63	0.86	24	MG
3	163	0.63	0.85	23	MG
4	53	0.37	0.81	12	empty
5	65	0.32	0.75	15	empty

Interfaces

6 interfaces between chains.

A–B · 1363 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 854 Å² buried · 21 hydrogen bonds · protein-nucleic
B–C · 823 Å² buried · 22 hydrogen bonds · protein-nucleic
B–D · 683 Å² buried · 13 hydrogen bonds · protein-nucleic
A–C · 645 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

4M30 · Crystal structure of RNASE III complexed with double-stranded RNA AND AMP (TYPE II… · the same entry in another collection · chain B against B, 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 4M30 · PDBe 4M30 · UniProt O67082

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