MolNFT v1 · #183057 · protein

Crystal structure of ZC3H12C pin domain with MG2+ ion

7NDI · Probable ribonuclease ZC3H12C: “Crystal structure of ZC3H12C pin domain with MG2+ ion”. X-ray diffraction, 2 ligands (MG, NA), 5 pockets (best druggability 0.57). MolNFT v1 #183057 on GenesisL1: 3D structure, binding sites and…

PDB: 7NDI
Type: protein
Length: 659 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ribonuclease ZC3H12C
EC: 3.1.-.-
UniProt: Q5DTV4
Ligands: MG, NA
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Probable ribonuclease ZC3H12C (EC 3.1.-.-)	protein	165	38% helix, 24% strand	Q5DTV4
D	Probable ribonuclease ZC3H12C (EC 3.1.-.-)	protein	164	38% helix, 24% strand	Q5DTV4

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 3 copies · chains A, C, D
EDO · 1,2-ethanediol · additive · 3 copies · chains A, C

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

Pockets

5 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	370	0.57	0.75	33	empty
2	230	0.55	0.78	33	EDO
3	270	0.55	0.76	34	empty
4	239	0.47	0.74	35	empty
5	52	0.23	0.71	15	MG

Interfaces

3 interfaces between chains.

A–C · 910 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 849 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 471 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7NDI · Crystal structure of ZC3H12C PIN domain with Mg2+ Ion · the same entry in another collection · chain A against A, TM-score 1.00
Q5DTV4 · AlphaFold monomer V2.0 prediction for probable ribonuclease ZC3H12C (Q5DTV4) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 Q5DTV4
Elsewhere: RCSB PDB 7NDI · PDBe 7NDI · UniProt Q5DTV4

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