MolNFT v1 · #37853 · protein + DNA

Crystal structure of a P53 core dimer bound to DNA

2GEQ · 5'- D(*GP*CP*GP*TP*GP*AP*GP*CP*AP*TP*GP*CP*TP*CP*AP*C)-3': “Crystal structure of a P53 core dimer bound to DNA”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.77). MolNFT v1 #37853 on GenesisL1: 3D structure…

PDB: 2GEQ
Type: protein + DNA
Length: 405 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- D(*GP*CP*GP*TP*GP*AP*GP*CP*AP*TP*GP*CP*TP*CP*AP*C)-3'; Cellular tumor antigen P53
UniProt: P02340
Ligands: ZN
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'- D(GPCPGPTPGPAPGPCPAPTPGPCPTPCPAPC)-3'	dna	15	—	—
D	5'- D(GPCPGPTPGPAPGPCPAPTPGPCPTPCPAPC)-3'	dna	13	—	—
A	Cellular tumor antigen P53	protein	188	9% helix, 36% strand	P02340
B	Cellular tumor antigen P53	protein	189	12% helix, 36% strand	P02340

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

7 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	344	0.77	0.88	34	empty
2	171	0.42	0.73	21	empty
3	140	0.40	0.74	18	empty
4	89	0.35	0.75	15	empty
5	133	0.35	0.72	22	empty

Interfaces

6 interfaces between chains.

C–D · 601 Å² buried · 51 hydrogen bonds · nucleic-nucleic
D–B · 326 Å² buried · 7 hydrogen bonds · protein-nucleic
C–A · 326 Å² buried · 7 hydrogen bonds · protein-nucleic
A–B · 322 Å² buried · 2 hydrogen bonds · protein-protein
C–B · 103 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

2GEQ · Crystal Structure of a p53 Core Dimer Bound to DNA · the same entry in another collection · chain C against C, 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 0.99

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 2GEQ · PDBe 2GEQ · UniProt P02340

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