MolNFT v1 · #163975 · protein + RNA

ZC3H12B-ribonuclease domain bound to RNA

6SJD · Probable ribonuclease ZC3H12B: “ZC3H12B-ribonuclease domain bound to RNA”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.68). MolNFT v1 #163975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SJD
Type: protein + RNA
Length: 363 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ribonuclease ZC3H12B; RNA (5'- R(*UP*GP*CP*GP*AP*CP*AP*GP*UP*CP*GP*GP*UP*AP*GP*CP…
EC: 3.1.-.-
UniProt: Q5HYM0
Ligands: MG
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Probable ribonuclease ZC3H12B (EC 3.1.-.-)	protein	168	38% helix, 20% strand	Q5HYM0
A	Probable ribonuclease ZC3H12B (EC 3.1.-.-)	protein	178	35% helix, 19% strand	Q5HYM0
D	RNA (5'- R(UPGPCPGPAPCPAPGPUPCPGPGPUPAPGPCP*A)-3')	rna	17	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, D, A
CAC · Cacodylate ion · additive · chains D

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	670	0.68	0.77	46	MG
2	298	0.63	0.80	44	empty

Interfaces

2 interfaces between chains.

B–A · 1070 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 458 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

6SJD · ZC3H12B-ribonuclease domain bound to RNA · the same entry in another collection · chain B against B, TM-score 1.00
Q5HYM0 · AlphaFold monomer V2.0 prediction for probable ribonuclease ZC3H12B (Q5HYM0) · a predicted model of the same protein · chain B 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 Q5HYM0
Elsewhere: RCSB PDB 6SJD · PDBe 6SJD · UniProt Q5HYM0

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