7NMI: Transactivation domain of p53

Transactivation domain of p53 in complex with S100P, using annexin A2 as crystallization chaperone. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Mar 2022.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,374
Mol. weight: 62.5 kDa
Ligands: CA
Released: 2 Mar 2022

Explore 7NMI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NMI contains 31 α-helices and 5 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	22-25	4
α-helix	37-43	7
α-helix	47-53	7

Chain B: 28 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-19	17
β-strand	27-28	2	1
α-helix	30-40	11
α-helix	53-61	9
β-strand	69-70	2	1
α-helix	71-91	21
α-helix	106-121	16
β-strand	123-125	3	2
β-strand	128-131	4	2
α-helix	133-143	11
α-helix	156-164	9
β-strand	172-173	2	2
α-helix	174-193	20
α-helix	207-219	13
α-helix	225-232	8
α-helix	237-251	15
α-helix	255-262	8
α-helix	265-275	11
α-helix	278-290	13
α-helix	297-306	10
α-helix	309-323	15
α-helix	327-334	8
α-helix	337-347	11
α-helix	351-353	3
α-helix	360-373	14
α-helix	382-391	10
α-helix	394-407	14
α-helix	412-419	8
α-helix	422-451	30
α-helix	457-467	11
α-helix	472-483	12
α-helix	487-494	8
α-helix	497-507	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cellular tumor antigen p53	A	protein	40	Homo sapiens	P04637 (AlphaFold model)
S100P-ANXA2 chimera	B	protein	512	Homo sapiens	P07355 (AlphaFold model), P25815 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7NMI_1 Cellular tumor antigen p53 (chains A)
ETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTE

Sequence of entity 2 (B), FASTA

>7NMI_2 S100P-ANXA2 chimera (chains B)
HMTELETAMGMIIDVFSRYSGSEGSTQTLTKGELKVLMEKELPGFLQSGKDKDAVDKLLK
DLDANGDAQVDFSEFIVFVAAITSACHKYFEKAGLKGGGGSGGSMTELETAMGMIIDVFS
RYSGSEGSTQTLTKGELKVLMEKELPGFLQSGKDKDAVDKLLKDLDANGDAQVDFSEFIV
FVAAITSACHKYFEKAGLKTSAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQ
RQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDS
LIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVID
YELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKE
VKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEF
KRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	9

Water and common crystallization additives (GOL) are not listed.

Primary citation

Transactivation domain of p53 in complex with S100P using annexin A2 as a crystallization chaperone. Ecsedi, P., Nyitray, L. To be published.

Other PDB entries of the same protein (UniProt P04637 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9C5S 1.01 Å, Disulfide-linked, antiparallel p53-derived peptide dimer (CV1)
3D06 1.2 Å, Human p53 core domain with hot spot mutation R249S (I)
5MHC 1.2 Å, Crystal structure of 14-3-3sigma and a p53 C-terminal 12-mer synthetic phosphopeptide
8UQR 1.22 Å, Crystal structure of the human p53 tetramerization domain
6GGC 1.24 Å, p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320
6SHZ 1.24 Å, p53 cancer mutant Y220C
4MZI 1.25 Å, Crystal structure of a human mutant p53
6GGE 1.25 Å, p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9327
3LW1 1.28 Å, Binary complex of 14-3-3 sigma and p53 pT387-peptide
5O1E 1.3 Å, p53 cancer mutant Y220C im complex with compound MB577
6RL3 1.3 Å, Fragment AZ-003 binding at the p53pT387/14-3-3 sigma interface
8E7A 1.3 Å, Crystal structure of the p53 (Y107H) core domain orthorhombic P form

Browse structure collections

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