9YC5: Human uPAR

Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1. Determined by electron microscopy at 2.94 Å resolution. Released 4 Feb 2026.

Method: Electron microscopy
Resolution: 2.94 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 4,689
Mol. weight: 80.28 kDa
Ligands: NAG
Released: 4 Feb 2026

Explore 9YC5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YC5 contains 20 α-helices and 57 β-strands across 3 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: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	94-96	3	1
β-strand	98-99	2	2
α-helix	100-102	3
β-strand	112-114	3	1
β-strand	121-129	9	2
β-strand	142-148	7	2
β-strand	157-160	4	2
β-strand	164-171	8	2
β-strand	189-196	8	3
β-strand	197-199	3	2
β-strand	200	1	4
β-strand	203-204	2	4
β-strand	211-216	6	3
β-strand	221-229	9	2
β-strand	235-242	8	2
α-helix	244-248	5
α-helix	253-256	4
β-strand	258-266	9	2
α-helix	274-276	3

Chain H: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
β-strand	11-12	2	6
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	33-39	7	7
β-strand	45-52	8	7
α-helix	54-56	3
β-strand	57-60	4	7
β-strand	68-73	6	5
β-strand	78-83	6	5
α-helix	88-90	3
β-strand	93-99	7	7
β-strand	114-115	2	6
β-strand	125-128	4	8
β-strand	141-151	11	8
β-strand	160	1	9
α-helix	161-163	3
β-strand	165	1	9
β-strand	169-171	3	8
α-helix	172-174	3
β-strand	175	1	8
β-strand	181-190	10	8
α-helix	191-193	3

Chain L: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	10
β-strand	10	1	11
β-strand	13	1	12
β-strand	21-24	4	10
β-strand	36-39	4	13
β-strand	48-49	2	13
α-helix	53-55	3
β-strand	62-65	4	10
β-strand	72-75	4	10
α-helix	80-82	3
β-strand	86-89	4	13
β-strand	102	1	13
β-strand	103	1	11
α-helix	105	1
β-strand	106	1	12
α-helix	107	1
α-helix	111-113	3
β-strand	114-116	3	14
α-helix	118-120	3
α-helix	123-126	4
β-strand	129-130	2	15
β-strand	133-139	7	14
α-helix	144-145	2
β-strand	146	1	16
β-strand	149	1	17
β-strand	154	1	17
α-helix	156-158	3
β-strand	159-164	6	14
β-strand	173-179	7	14
β-strand	181-182	2	15
α-helix	183-186	4
β-strand	193	1	17
β-strand	194-195	2	18
β-strand	196	1	16
β-strand	206-207	2	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Urokinase plasminogen activator surface receptor	A	protein	283	Homo sapiens	Q03405 (AlphaFold model)
Anti-uPAR antibody FL1 Fab heavy chain	H	protein	221	Mus musculus
Anti-uPAR antibody FL1 Fab light chain	L	protein	219	Mus musculus

Sequence of entity 1 (A), FASTA

>9YC5_1 Urokinase plasminogen activator surface receptor (chains A)
LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTG
LKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEE
QCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGP
ILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRG
CATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSG

Sequence of entity 2 (H), FASTA

>9YC5_2 Anti-uPAR antibody FL1 Fab heavy chain (chains H)
EVQLQQSGSVLVRPGTSVNLSCKASGYTFTSYWMSWVKQRPGQGLEWIGEIFPKSGRINS
NENFRGKATLTVDTSSSTAYINLSSLTSEDSAVYYCSPIYSGDYGFADWGQGTLVTVSAA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (L), FASTA

>9YC5_3 Anti-uPAR antibody FL1 Fab light chain (chains L)
DIVMTQTPLSLPVSLGDQASISCRSSQSVVSNNGKTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEVKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural basis for uPAR binding to an antibody developed for targeted cancer therapy. Mechanistic insights into flexibility, ligand recognition, and molecular imaging. Anane, R.F., Kumari, A., Venugopal, H. et al. Protein Sci (2026) 35:e70473-e70473. DOI 10.1002/pro.70473 · PubMed

Other PDB entries of the same protein (UniProt Q03405 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FD6 1.9 Å, Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor…
3U74 2.39 Å, Crystal structure of stabilized human uPAR mutant
3BT2 2.5 Å, Structure of urokinase receptor, urokinase and vitronectin complex
1YWH 2.7 Å, crystal structure of urokinase plasminogen activator receptor
2I9B 2.8 Å, Crystal structure of ATF-urokinase receptor complex
3BT1 2.8 Å, Structure of urokinase receptor, urokinase and vitronectin complex
7V63 2.91 Å, Structure of dimeric uPAR at low pH
7E17 2.96 Å, Structure of dimeric uPAR
4QTI 3.0 Å, Crystal structure of human uPAR in complex with anti-uPAR Fab 8B12
3U73 3.19 Å, Crystal structure of stabilized human uPAR mutant in complex with ATF
4K24 4.5 Å, Structure of anti-uPAR Fab ATN-658 in complex with uPAR
9YC6 4.8 Å, Mutant human uPAR bound to the Fab fragment of the targeted cancer therapeutic antibody…

Browse structure collections

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