7PSQ | pdb_00007psq

Crystal structure of S100A4 labeled with NU074381b.

PDB DOI: https://doi.org/10.2210/pdb7PSQ/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-09-23 Released: 2022-10-05
Deposition Author(s): Giroud, C., Szommer, T., Coxon, C., Monteiro, O., Christott, T., Bennett, J., Aitmakhanova, K., Raux, B., Newman, J., Elkins, J., Krojer, T., Arruda Bezerra, G., Koekemoer, L., Bountra, C., Von Delft, F., Brennan, P., Fedorov, O.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.236 (Depositor), 0.243 (DCC)
R-Value Work:
0.205 (Depositor), 0.213 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of S100A4 labeled with NU074381b.

Giroud, C., Szommer, T., Coxon, C., Monteiro, O., Christott, T., Bennett, J., Aitmakhanova, K., Raux, B., Newman, J., Elkins, J., Krojer, T., Koekemoer, L., Von Delft, F., Bountr, C., Brennan, P., Fedorov, O.

To be published.

Macromolecule Content

Total Structure Weight: 58.52 kDa
Atom Count: 3,426
Modeled Residue Count: 410
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A4	A, B [auth C], C [auth E], D [auth G]	123	Homo sapiens	Mutation(s): 0 Gene Names: S100A4, CAPL, MTS1
UniProt & NIH Common Fund Data Resources
Find proteins for P26447 (Homo sapiens) Explore P26447 Go to UniProtKB: P26447
PHAROS: P26447 GTEx: ENSG00000196154
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26447
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
82Q (Subject of Investigation/LOI) Query on 82Q Download:Ideal Coordinates CCD File SDF format, chain O [auth G] SDF format, chain L [auth E] MOL2 format, chain O [auth G] MOL2 format, chain L [auth E] mmCIF format, chain O [auth G] mmCIF format, chain L [auth E]	L [auth E], O [auth G]	(2~{R},4~{R})-1-ethanoyl-~{N}-naphthalen-1-yl-4-phenyl-pyrrolidine-2-carboxamide C₂₃ H₂₂ N₂ O₂ HXZFWDRYUUGFOU-SIKLNZKXSA-N		Interactions Focus chain L [auth E] Focus chain O [auth G] Interactions & Density Focus chain L [auth E] Focus chain O [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain J [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C]	G [auth A], J [auth C], K [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth G] SDF format, chain Q [auth G] SDF format, chain P [auth G] SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain I [auth C] SDF format, chain H [auth C] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth G] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth G] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth C] I [auth C] M [auth E] E [auth A], F [auth A], H [auth C], I [auth C], M [auth E], N [auth E], P [auth G], Q [auth G], R [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G]