7NMI | pdb_00007nmi

Transactivation domain of p53 in complex with S100P, using annexin A2 as crystallization chaperone

PDB DOI: https://doi.org/10.2210/pdb7NMI/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-02-23 Released: 2022-03-02
Deposition Author(s): Ecsedi, P., Nyitray, L.
Funding Organization(s): National Research Development and Innovation Office (NKFIH)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.194 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Transactivation domain of p53 in complex with S100P using annexin A2 as a crystallization chaperone

Ecsedi, P., Nyitray, L.

To be published.

Macromolecule Content

Total Structure Weight: 62.5 kDa
Atom Count: 4,374
Modeled Residue Count: 520
Deposited Residue Count: 552
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A	40	Homo sapiens	Mutation(s): 0 Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637 Go to UniProtKB: P04637
PHAROS: P04637 GTEx: ENSG00000141510
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04637
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S100P-ANXA2 chimera	B	512	Homo sapiens	Mutation(s): 1 Gene Names: S100P, S100E, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D
UniProt & NIH Common Fund Data Resources
Find proteins for P07355 (Homo sapiens) Explore P07355 Go to UniProtKB: P07355
PHAROS: P07355 GTEx: ENSG00000182718
Find proteins for P25815 (Homo sapiens) Explore P25815 Go to UniProtKB: P25815
PHAROS: P25815 GTEx: ENSG00000163993
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P07355P25815
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth B]	D [auth B] E [auth B] F [auth B] G [auth B] H [auth B] D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]