MolNFT v1 · #109517 · protein

Human PARP13 (ZC3HAV1), C-terminal parp domain (H810N; N830Y variant)

4X52 · Zinc finger ccch-type antiviral protein 1: “Human PARP13 (ZC3HAV1), C-terminal parp domain (H810N; N830Y variant)”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.59). MolNFT v1 #109517 on GenesisL1: 3D structure…

PDB: 4X52
Type: protein
Length: 682 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Zinc finger ccch-type antiviral protein 1
UniProt: Q7Z2W4
Ligands: SO4
Pockets: 6 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Zinc finger ccch-type antiviral protein 1	protein	171	28% helix, 33% strand	Q7Z2W4
C, D	Zinc finger ccch-type antiviral protein 1	protein	170	28% helix, 34% strand	Q7Z2W4

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, D, B, C
GOL · Glycerol · additive · 2 copies · chains A, C, B, D

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

Pockets

6 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	385	0.59	0.76	46	empty
2	347	0.56	0.75	35	empty
3	149	0.48	0.78	31	empty
4	134	0.46	0.78	27	GOL
5	115	0.43	0.77	23	GOL

Interfaces

4 interfaces between chains.

B–D · 713 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 667 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 461 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 450 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4X52 · Human PARP13 (ZC3HAV1), C-Terminal PARP Domain (H810N; N830Y variant) · the same entry in another collection · chain A against A, TM-score 1.00
Q7Z2W4 · AlphaFold monomer V2.0 prediction for zinc finger ccch-type antiviral protein 1 (Q7Z2W4) · 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 Q7Z2W4
Elsewhere: RCSB PDB 4X52 · PDBe 4X52 · UniProt Q7Z2W4

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