4RG2: Tumor suppressor p53-binding protein 1

Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand. Determined by X-ray diffraction at 1.5 Å resolution. Released 15 Oct 2014.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,323
Mol. weight: 28.74 kDa
Ligands: 3OO
Released: 15 Oct 2014

Explore 4RG2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RG2 contains 9 α-helices and 28 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1490-1494	5	1
β-strand	1501-1509	9	1
β-strand	1514-1519	6	1
β-strand	1524-1528	5	1
α-helix	1529-1531	3
β-strand	1532-1533	2	1
α-helix	1538-1539	2
β-strand	1543-1546	4	2
β-strand	1548	1	3
β-strand	1551	1	3
β-strand	1555-1564	10	2
β-strand	1567-1574	8	2
β-strand	1577-1582	6	2
α-helix	1583-1585	3
β-strand	1586-1587	2	2
β-strand	1588	1	1
α-helix	1590-1600	11
β-strand	1601	1	1

Chain B: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1490-1494	5	4
β-strand	1501-1511	11	4
β-strand	1514-1519	6	4
β-strand	1524-1528	5	4
α-helix	1529-1531	3
β-strand	1532-1533	2	4
α-helix	1538-1539	2
β-strand	1543-1546	4	5
β-strand	1548	1	6
β-strand	1551	1	6
β-strand	1555-1564	10	5
β-strand	1567-1574	8	5
β-strand	1577-1582	6	5
α-helix	1583-1585	3
β-strand	1586-1587	2	5
β-strand	1588	1	4
α-helix	1590-1594	5
α-helix	1597-1600	4
β-strand	1601	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor suppressor p53-binding protein 1	A, B	protein	125	Homo sapiens	Q12888 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4RG2_1 Tumor suppressor p53-binding protein 1 (chains A, B)
GGNSFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLD
TEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYG
LGPYE

Ligands and cofactors

ID	Name	Formula	Copies
3OO	3-bromo-N-[3-(tert-butylamino)propyl]benzamide	C14 H21 Br N2 O	1

Water and common crystallization additives (EDO, UNX) are not listed.

Primary citation

Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1. Perfetti, M.T., Baughman, B.M., Dickson, B.M. et al. ACS Chem Biol (2015) 10:1072-1081. DOI 10.1021/cb500956g · PubMed

Other PDB entries of the same protein (UniProt Q12888 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SVI 1.15 Å, Ubiquitin variant i53:Mutant L67H with 53BP1 Tudor domain
8SVH 1.16 Å, Ubiquitin variant i53 mutant L67R bound to 53BP1 Tudor Domain
8SVG 1.21 Å, Ubiquitin variant i53 in complex with 53BP1 Tudor domain
2G3R 1.25 Å, Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution
6VA5 1.28 Å, Tudor Domain of Tumor suppressor p53BP1 with MFP-4184
6VIP 1.36 Å, Tudor domain of tumor suppressor P53BP1 with mfp-6008
7LIN 1.44 Å, X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide
3LGF 1.5 Å, Crystal structure of the 53BP1 tandem tudor domain in complex with p53K370me2
8SVJ 1.5 Å, Ubiquitin variant i53: mutant VHH with 53BP1 Tudor domain
8F0W 1.52 Å, Tudor Domain of Tumor suppressor p53BP1 with MFP-5956
3LGL 1.6 Å, Crystal structure of the 53BP1 tandem tudor domain in complex with p53K382me2
8SWJ 1.6 Å, Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC8531

Browse structure collections

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