MolNFT v1 · #67306 · protein + DNA

Diversity in DNA recognition by P53 revealed by crystal structures with hoogsteen base pairs (P53-DNA complex 2)

3IGK · Cellular tumor antigen P53: “Diversity in DNA recognition by P53 revealed by crystal structures with hoogsteen base pairs (P53-DNA complex…”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.37). MolNFT v1 #67306 on…

PDB: 3IGK
Type: protein + DNA
Length: 208 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cellular tumor antigen P53; DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
UniProt: P04637
Ligands: ZN
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cellular tumor antigen P53	protein	197	12% helix, 34% strand	P04637
B	DNA (5'-D(CPGPGPGPCPAPTPGPCPCPCPG)-3')	dna	11	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

2 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	91	0.37	0.75	19	empty
2	56	0.25	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 237 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3IGK · Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base… · the same entry in another collection · chain A against A, TM-score 1.00

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 P04637
Elsewhere: RCSB PDB 3IGK · PDBe 3IGK · UniProt P04637

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