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Tudor domain of tumor suppressor P53BP1 with mfp-6008

Analyse Tudor domain of tumor suppressor P53BP1 with mfp-6008 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VIP
Type: protein
Length: 241 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TP53-binding protein 1
UniProt: Q12888
Ligands: QXY, UNX
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TP53-binding protein 1	protein	120	13% helix, 53% strand	Q12888
B	TP53-binding protein 1	protein	121	14% helix, 50% strand	Q12888

Ligands and binding sites

QXY · {4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]phenyl}(4-ethylpiperazin-1-yl)methanone · ligand · 2 copies · chains A, B
UNX · Unknown atom or ion · ion · 4 copies · chains A, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.49	0.75	34	UNX

Interfaces

1 interface between chains.

A–B · 472 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6VIP · Tudor domain of tumor suppressor P53BP1 with mfp-6008 · 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 Q12888
Elsewhere: RCSB PDB 6VIP · PDBe 6VIP · UniProt Q12888

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