27UH: De novo-designed VHH targeting S100A4

Crystal structure of a de novo-designed VHH targeting S100A4. Determined by X-ray diffraction at 1.82 Å resolution. Released 5 Aug 2026.

Method: X-ray diffraction
Resolution: 1.82 Å
Organisms: synthetic construct, Homo sapiens
Chains: 8
Atoms: 6,907
Mol. weight: 103.45 kDa
Ligands: CA
Released: 5 Aug 2026

Explore 27UH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

27UH contains 28 α-helices and 52 β-strands across 8 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	10-12	3	2
β-strand	18-26	9	1
β-strand	31-39	9	2
β-strand	46-52	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-101	10	2
β-strand	106-110	5	2
β-strand	114-118	5	2

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-19	17
β-strand	28	1	3
α-helix	30-40	11
α-helix	42-45	4
α-helix	51-61	11
β-strand	69	1	3
α-helix	71-87	17

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
β-strand	10-12	3	5
β-strand	18-26	9	4
β-strand	31-39	9	5
β-strand	45-52	8	5
β-strand	58-60	3	5
β-strand	68-73	6	4
α-helix	74-76	3
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-102	11	5
β-strand	105-110	6	5
β-strand	114-118	5	5

Chains D and H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-19	17
β-strand	28	1	6
α-helix	30-40	11
α-helix	42-45	4
α-helix	51-61	11
β-strand	69	1	6
α-helix	71-90	20

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
β-strand	10-12	3	8
β-strand	18-26	9	7
β-strand	31-40	10	8
β-strand	44-52	9	8
β-strand	58-60	3	8
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-101	10	8
β-strand	106-110	5	8
β-strand	114-118	5	8

Chain F: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-19	17
β-strand	27-28	2	9
α-helix	30-40	11
α-helix	51-61	11
β-strand	69-70	2	9
α-helix	71-91	21

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	10-12	3	11
β-strand	18-26	9	10
β-strand	31-39	9	11
β-strand	45-52	8	11
β-strand	58-60	3	11
α-helix	62-64	3
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-102	11	11
β-strand	105-110	6	11
β-strand	114-118	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S100A4_VHH-N20	A, C, E, G	protein	131	synthetic construct
Protein S100-A4	B, D, F, H	protein	102	Homo sapiens	P26447 (AlphaFold model)

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

>27UH_1 S100A4_VHH-N20 (chains A, C, E, G)
EVQLVESGGGLVQPGGSLRLSCAASGDTSFIIAMAWYRQAPGKGRELVAGLNRLTSSISY
ADSVKGRFTISRDNAKNTLYLQMNSLRPEDTAVYYCAAARVLGGTTERAWGQGTLVTVSS
GGGGSHHHHHH

Sequence of entity 2 (B, D, F, H), FASTA

>27UH_2 Protein S100-A4 (chains B, D, F, H)
SMACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLM
SNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQPRKK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	8

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

Primary citation

High-Affinity Protein Binder Design via Flow Matching and In Silico Maturation. Yu, Q.L., Guo, L.Y., Qin, X.Y. 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
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
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.

Browse structure collections

About this viewer

MolViewer shows 27UH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.