Research workbench

Mouse NP95 sra domain non-specific DNA complex

Analyse Mouse NP95 sra domain non-specific DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZO2
Type: protein + DNA
Length: 225 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase UHRF1; DNA (5'- D(*DAP*DAP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DTP…
EC: 6.3.2.-
UniProt: Q8VDF2
Ligands: PO4
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-)	protein	201	20% helix, 26% strand	Q8VDF2
D, E	DNA (5'- D(DAPDAPDCPDTPDGPDCPDGPDCPDAPDGPDTPDT)-3')	dna	12	—	—

Ligands and binding sites

PO4 · Phosphate ion · ion · chains 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	266	0.59	0.79	39	empty
2	69	0.28	0.73	10	empty
3	56	0.26	0.73	13	empty

Interfaces

2 interfaces between chains.

D–E · 557 Å² buried · 39 hydrogen bonds · nucleic-nucleic
B–E · 277 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

2ZO2 · Mouse NP95 SRA domain non-specific DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
Q8VDF2 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UHRF1 (Q8VDF2) · 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 Q8VDF2
Elsewhere: RCSB PDB 2ZO2 · PDBe 2ZO2 · UniProt Q8VDF2

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