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Crystal structure of N-COLE7/12-bp DNA/ZN complex

Analyse Crystal structure of N-COLE7/12-bp DNA/ZN complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZNS
Type: protein + DNA
Length: 142 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3'; Colicin E7
EC: 3.1.-.-
UniProt: Q47112
Ligands: ZN
Pockets: 4 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, C	5'-D(CPGPGPGPAPTPAPTPCPCPCPG)-3'	dna	12	—	—
A	Colicin E7 (EC 3.1.-.-)	protein	118	37% helix, 17% strand	Q47112

Ligands and binding sites

ZN · Zinc ion · metal · chains B, A

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.46	0.81	17	empty
2	72	0.44	0.82	13	empty
3	111	0.41	0.77	16	empty
4	80	0.31	0.73	12	empty

Interfaces

3 interfaces between chains.

B–C · 498 Å² buried · 46 hydrogen bonds · nucleic-nucleic
B–A · 465 Å² buried · 14 hydrogen bonds · protein-nucleic
C–A · 456 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

1ZNS · Crystal structure of N-ColE7/12-bp DNA/Zn complex · the same entry in another collection · chain B against B, TM-score 1.00
Q47112 · AlphaFold monomer V2.0 prediction for colicin-E7 (Q47112) · 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 Q47112
Elsewhere: RCSB PDB 1ZNS · PDBe 1ZNS · UniProt Q47112

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