7PSQ: S100A4 labeled with NU074381b

Crystal structure of S100A4 labeled with NU074381b. Determined by X-ray diffraction at 1.91 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 1.91 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,426
Mol. weight: 58.52 kDa
Ligands: 82Q, CA
Released: 5 Oct 2022

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

Secondary structure: helices and β-sheets

7PSQ contains 22 α-helices and 8 β-strands across 4 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	29	1	1
α-helix	31-41	11
α-helix	43-45	3
α-helix	52-62	11
β-strand	70	1	1
α-helix	72-88	17

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	28-29	2	2
α-helix	31-41	11
α-helix	43-45	3
α-helix	52-62	11
β-strand	70-71	2	2
α-helix	72-90	19

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	29	1	3
α-helix	31-41	11
α-helix	43-45	3
α-helix	53-62	10
β-strand	70	1	3
α-helix	72-92	21
α-helix	93-95	3

Chain G: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	28-29	2	4
α-helix	31-41	11
α-helix	43-45	3
α-helix	52-62	11
β-strand	70-71	2	4
α-helix	72-92	21
α-helix	93-95	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein S100-A4	A, C, E, G	protein	123	Homo sapiens	P26447 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>7PSQ_1 Protein S100-A4 (chains A, C, E, G)
HMHHHHHHSSGVDLGTENLYFQSMACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKEL
LTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQ
PRK

Ligands and cofactors

ID	Name	Formula	Copies
82Q	(2~{R},4~{R})-1-ethanoyl-~{N}-naphthalen-1-yl-4-phenyl-pyrrolidine-2-carboxamide	C23 H22 N2 O2	2
CA	Calcium ion	Ca	9

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

Primary citation

Crystal structure of S100A4 labeled with NU074381b. Giroud, C., Szommer, T., Coxon, C. et al. To be published.

Other PDB entries of the same protein (UniProt P26447 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4CFQ 1.37 Å, Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with…
4CFR 1.4 Å, Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with non- muscle myosin IIA
3C1V 1.5 Å, The 1.5 A Crystal structure of Ca2+-bound S100A4
4ETO 1.54 Å, Structure of S100A4 in complex with non-muscle myosin-IIA peptide
2Q91 1.63 Å, Structure of the Ca2+-Bound Activated Form of the S100A4 Metastasis Factor
27UH 1.82 Å, Crystal structure of a de novo-designed VHH targeting S100A4
3ZWH 1.94 Å, Ca2+-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with myosin IIA
3CGA 2.03 Å, Crystal structure of metastasis-associated protein S100A4 in the active, calcium-bound…
5LPU 2.1 Å, Crystal structure of Annexin A2 complexed with S100A4
4HSZ 2.25 Å, Structure of truncated (delta8C) S100A4
3KO0 2.3 Å, Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor
7PSP 2.61 Å, Crystal structure of S100A4 labeled with NU000846b.

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