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An induced fit mechanism regulates P53 DNA binding kinetics to confer sequence specificity

Analyse An induced fit mechanism regulates P53 DNA binding kinetics to confer sequence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3Q01
Type: protein
Length: 466 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cellular tumor antigen P53
UniProt: P04637
Ligands: ZN
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cellular tumor antigen P53	protein	233	19% helix, 31% strand	P04637

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, 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	64	0.51	0.85	20	empty
2	114	0.41	0.76	21	empty
3	50	0.38	0.80	14	empty
4	105	0.37	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 1253 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

3Q01 · An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity · 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 3Q01 · PDBe 3Q01 · UniProt P04637

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