3KO0: Protein S100-A4

Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor. Determined by X-ray diffraction at 2.3 Å resolution. Released 26 May 2010.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 20
Atoms: 16,855
Mol. weight: 252.81 kDa
Ligands: TFP, CA
Released: 26 May 2010

Explore 3KO0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KO0 contains 101 α-helices and 40 β-strands across 20 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.

Chains A, B and I: 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	43-46	4
α-helix	52-62	11
β-strand	70	1	1
α-helix	72-90	19

Chains C, E, L and N: 5 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	43-46	4
α-helix	52-62	11
β-strand	70	1	3
α-helix	72-91	20

Chain D: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	28-29	2	4
α-helix	31-36	6
α-helix	37-41	5
α-helix	43-46	4
α-helix	53-62	10
β-strand	70-71	2	4
α-helix	72-91	20

Chain F: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	28-29	2	6
α-helix	31-41	11
α-helix	43-46	4
α-helix	53-62	10
β-strand	70-71	2	6
α-helix	72-91	20

Chain G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	29	1	7
α-helix	31-41	11
α-helix	43-46	4
α-helix	53-62	10
β-strand	70	1	7
α-helix	72-91	20

Chains H, J, K, M, O, P, R and S: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	28-29	2	8
α-helix	31-41	11
α-helix	43-46	4
α-helix	52-62	11
β-strand	70-71	2	8
α-helix	72-90	19

Chain Q: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	28-29	2	17
α-helix	31-41	11
α-helix	43-46	4
α-helix	56-62	7
β-strand	70-71	2	17
α-helix	72-90	19

Chain T: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	28-29	2	20
α-helix	31-41	11
α-helix	43-46	4
α-helix	52-62	11
β-strand	70-71	2	20
α-helix	72-91	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein S100-A4	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	protein	101	Homo sapiens	P26447 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T), FASTA

>3KO0_1 Protein S100-A4 (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T)
MACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMS
NLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQPRKK

Ligands and cofactors

ID	Name	Formula	Copies
TFP	10-[3-(4-methyl-piperazin-1-yl)-propyl]-2-trifluoromethyl-10H-phenothiazine	C21 H24 F3 N3 S	40
CA	Calcium ion	Ca	40

Primary citation

Phenothiazines inhibit S100A4 function by inducing protein oligomerization. Malashkevich, V.N., Dulyaninova, N.G., Ramagopal, U.A. et al. Proc Natl Acad Sci U S A (2010) 107:8605-8610. DOI 10.1073/pnas.0913660107 · PubMed

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
7PSQ 1.91 Å, Crystal structure of S100A4 labeled with NU074381b.
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
7PSP 2.61 Å, Crystal structure of S100A4 labeled with NU000846b.

Browse structure collections

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