9YC6: Mutant human uPAR

Mutant human uPAR bound to the Fab fragment of the targeted cancer therapeutic antibody FL1. Determined by electron microscopy at 4.8 Å resolution. Released 4 Feb 2026.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 5,515
Mol. weight: 80.66 kDa
Ligands: NAG
Released: 4 Feb 2026

Explore 9YC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YC6 contains 19 α-helices and 68 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 H: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
β-strand	11-12	2	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	33-39	7	16
β-strand	45-52	8	16
β-strand	57-60	4	16
β-strand	69-73	5	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	93-99	7	16
β-strand	114-115	2	15
β-strand	121	1	17
β-strand	125-128	4	18
β-strand	141-151	11	18
β-strand	152	1	17
β-strand	160	1	19
α-helix	161-163	3
β-strand	165	1	19
β-strand	169-171	3	18
α-helix	172-174	3
β-strand	175-176	2	18
β-strand	181-190	10	18

Chain L: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	10	1	2
β-strand	13	1	3
β-strand	21-24	4	1
β-strand	35-39	5	4
β-strand	48	1	4
α-helix	54-55	2
β-strand	64-65	2	1
β-strand	72-73	2	1
α-helix	80-82	3
β-strand	86-90	5	4
β-strand	97-98	2	4
α-helix	99-100	2
β-strand	102	1	4
β-strand	103	1	2
α-helix	105	1
β-strand	106	1	3
α-helix	107	1
α-helix	111-113	3
β-strand	114-116	3	5
α-helix	118-120	3
α-helix	123-126	4
β-strand	129-139	11	5
α-helix	144-145	2
β-strand	146	1	6
β-strand	149	1	7
β-strand	154	1	7
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-186	4
β-strand	193	1	7
β-strand	194-195	2	8
β-strand	196	1	6
β-strand	206-207	2	8

Chain U: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	12-16	5	9
α-helix	17-18	2
β-strand	23-33	11	9
β-strand	36-46	11	9
β-strand	53-55	3	9
β-strand	58	1	10
β-strand	63	1	10
β-strand	66-71	6	9
β-strand	94-97	4	11
β-strand	98-99	2	9
β-strand	111-114	4	11
β-strand	121-126	6	9
β-strand	128-129	2	9
β-strand	143-149	7	9
β-strand	155-160	6	9
β-strand	164-171	8	9
α-helix	184-186	3
α-helix	188	1
β-strand	189-196	8	12
β-strand	197-199	3	9
β-strand	200	1	13
β-strand	204	1	13
β-strand	211-216	6	12
β-strand	221-229	9	9
β-strand	235	1	9
β-strand	237-242	6	9
α-helix	253-256	4
β-strand	258-266	9	9

Molecules and chains

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

Sequence of entity 1 (L), FASTA

>9YC6_1 Anti-uPAR antibody FL1 Fab light chain (chains L)
DIVMTQTPLSLPVSLGDQASISCRSSQSVVSNNGKTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEVKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (U), FASTA

>9YC6_2 Urokinase plasminogen activator surface receptor (chains U)
LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTCSEKTNRTLSYRTG
LKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEE
QCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGP
ILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRG
CATASMCQHAHLGDAFSMCHIDVSCCTKSGCNHPDLDVQYRSG

Sequence of entity 3 (H), FASTA

>9YC6_3 Anti-uPAR antibody FL1 Fab heavy chain (chains H)
EVQLQQSGSVLVRPGTSVNLSCKASGYTFTSYWMSWVKQRPGQGLEWIGEIFPKSGRINS
NENFRGKATLTVDTSSSTAYINLSSLTSEDSAVYYCSPIYSGDYGFADWGQGTLVTVSAA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

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
9YC5 2.94 Å, Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1
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

Browse structure collections

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