6T58: PDB entry 6T58

Structure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone. Determined by X-ray diffraction at 3.1 Å resolution. Released 27 May 2020.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,597
Mol. weight: 127.38 kDa
Ligands: CA
Released: 27 May 2020

Explore 6T58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T58 contains 53 α-helices and 4 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: 33 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	37-41	5
α-helix	47-52	6
α-helix	65-81	17
β-strand	90	1	1
α-helix	92-102	11
α-helix	115-123	9
β-strand	131	1	1
α-helix	133-146	14
α-helix	163-179	17
β-strand	188	1	2
α-helix	190-199	10
α-helix	211-221	11
β-strand	229	1	2
α-helix	231-249	19
α-helix	254-257	4
α-helix	261-272	12
α-helix	279-286	8
α-helix	291-305	15
α-helix	309-315	7
α-helix	320-329	10
α-helix	332-344	13
α-helix	351-360	10
α-helix	363-377	15
α-helix	381-388	8
α-helix	391-401	11
α-helix	405-407	3
α-helix	414-427	14
α-helix	436-445	10
α-helix	448-461	14
α-helix	466-473	8
α-helix	476-490	15
α-helix	492-505	14
α-helix	511-520	10
α-helix	526-537	12
α-helix	541-548	8
α-helix	551-561	11

Chain B: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	261-272	12
α-helix	279-286	8
α-helix	291-304	14
α-helix	309-316	8
α-helix	320-329	10
α-helix	332-343	12
α-helix	351-358	8
α-helix	363-377	15
α-helix	381-388	8
α-helix	391-401	11
α-helix	414-427	14
α-helix	436-445	10
α-helix	448-458	11
α-helix	466-473	8
α-helix	477-490	14
α-helix	492-505	14
α-helix	511-520	10
α-helix	526-537	12
α-helix	541-548	8
α-helix	551-560	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2	A, B	protein	553	Homo sapiens	P04637 (AlphaFold model), P07355 (AlphaFold model), P26447 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6T58_1 Cellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2 (chains A, B)
GSHMETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEGGSGHMACPLEKALDV
MVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVD
FQEYCVFLSCIAMMCNEFFEGFSAGSAGACPLEKALDVMVSTFHKYSGKEGDKFKLNKSE
LKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGF
TSAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASA
LKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRV
YKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRK
GTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNK
PLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGD
YQKALLYLCGGDD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	16

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

Primary citation

Structure Determination of the Transactivation Domain of p53 in Complex with S100A4 Using Annexin A2 as a Crystallization Chaperone. Ecsedi, P., Gogl, G., Hof, H. et al. Structure (2020) 28:943-953.e4. DOI 10.1016/j.str.2020.05.001 · PubMed

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

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