MolNFT v1 · #120740 · protein

Crystal structure of regnase pin domain, form II

5H9W · Ribonuclease ZC3H12A: “Crystal structure of regnase pin domain, form II”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.59). MolNFT v1 #120740 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H9W
Type: protein
Length: 324 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease ZC3H12A
EC: 3.1.-.-
UniProt: Q5D1E7
Ligands: NA
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribonuclease ZC3H12A (EC 3.1.-.-)	protein	162	39% helix, 24% strand	Q5D1E7

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	311	0.59	0.78	38	empty
2	94	0.33	0.73	21	empty
3	63	0.30	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 965 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5H9W · Crystal structure of Regnase PIN domain, form II · the same entry in another collection · chain A against A, TM-score 1.00
Q5D1E7 · AlphaFold monomer V2.0 prediction for endoribonuclease ZC3H12A (Q5D1E7) · a predicted model of the same protein · chain A 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 Q5D1E7
Elsewhere: RCSB PDB 5H9W · PDBe 5H9W · UniProt Q5D1E7

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