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P53 DNA binding domain in complex with NB139

Analyse P53 DNA binding domain in complex with NB139 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QO1
Type: protein
Length: 326 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NB139 nanobody against the DNA-binding domain of P53; Cellular tumor antigen P53
UniProt: P04637
Ligands: ZN
Pockets: 1 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NB139 nanobody against the DNA-binding domain of P53	protein	127	11% helix, 48% strand	—
B	Cellular tumor antigen P53	protein	199	9% helix, 34% strand	P04637

Ligands and binding sites

ZN · Zinc ion · metal · chains B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	245	0.61	0.81	47	empty

Interfaces

1 interface between chains.

A–B · 508 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4QO1 · p53 DNA binding domain in complex with Nb139 · 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 4QO1 · PDBe 4QO1 · UniProt P04637

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