MolNFT v1 · #63042 · protein + DNA

Crystal structure of a P53 core tetramer bound to DNA

3EXJ · Mouse P53 core domain: “Crystal structure of a P53 core tetramer bound to DNA”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.73). MolNFT v1 #63042 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EXJ
Type: protein + DNA
Length: 411 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mouse P53 core domain; 5'-D(P*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'…
UniProt: P02340
Ligands: ZN
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mouse P53 core domain	protein	194	12% helix, 35% strand	P02340
B	Mouse P53 core domain	protein	194	12% helix, 35% strand	P02340
C	5'-D(PDGPDAPDGPDCPDAPDTPDGPDCPDTPDCP*DA)-3'	dna	11	—	—
D	5'-D(DTPDTPDGPDAPDGPDCPDAPDTPDGPDCPDTPDC)-3'	dna	12	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
FLC · Citrate anion · additive · chains B

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

Pockets

4 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	479	0.73	0.82	52	empty
2	164	0.47	0.77	23	empty
3	140	0.45	0.77	23	empty
4	52	0.31	0.76	18	empty

Interfaces

6 interfaces between chains.

C–D · 505 Å² buried · 46 hydrogen bonds · nucleic-nucleic
A–C · 367 Å² buried · 7 hydrogen bonds · protein-nucleic
A–B · 344 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 332 Å² buried · 7 hydrogen bonds · protein-nucleic
A–D · 249 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

3EXJ · Crystal Structure of a p53 Core Tetramer Bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
P02340 · AlphaFold monomer V2.0 prediction for cellular tumor antigen P53 (P02340) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P02340
Elsewhere: RCSB PDB 3EXJ · PDBe 3EXJ · UniProt P02340

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