1YWH: Urokinase plasminogen activator receptor

crystal structure of urokinase plasminogen activator receptor. Determined by X-ray diffraction at 2.7 Å resolution. Released 10 May 2005.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 16
Atoms: 18,552
Mol. weight: 304.71 kDa
Ligands: NAG
Released: 10 May 2005

Explore 1YWH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YWH contains 52 α-helices and 169 β-strands across 16 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: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
α-helix	17-18	2
β-strand	23-33	11	1
β-strand	36-46	11	1
β-strand	53-58	6	1
β-strand	63-71	9	1
β-strand	94-96	3	2
β-strand	98	1	1
α-helix	105-108	4
β-strand	112-114	3	2
β-strand	121-129	9	1
β-strand	142-149	8	1
β-strand	155-160	6	1
β-strand	164-171	8	1
α-helix	184-186	3
β-strand	189-196	8	3
β-strand	197-199	3	1
β-strand	200	1	4
β-strand	204	1	4
α-helix	207-209	3
β-strand	211-216	6	3
β-strand	221-227	7	1
β-strand	236-242	7	1
α-helix	244-247	4
α-helix	250-253	4
β-strand	262-266	5	1

Chains B and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	504-510	7

Chain C: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
β-strand	12-16	5	5
β-strand	23-30	8	5
β-strand	32-33	2	6
β-strand	36-37	2	6
β-strand	40-46	7	5
β-strand	53-58	6	5
β-strand	63-71	9	5
β-strand	94-96	3	7
β-strand	98	1	5
β-strand	112-114	3	7
β-strand	121-129	9	5
β-strand	142-149	8	5
β-strand	155-160	6	5
β-strand	164-171	8	5
α-helix	181-182	2
α-helix	184-186	3
β-strand	189-196	8	8
β-strand	197-199	3	5
β-strand	211-216	6	8
β-strand	221-228	8	5
β-strand	235-242	8	5
α-helix	244-247	4
α-helix	250-253	4
β-strand	259-266	8	5

Chains D, H, J, L, N and P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	504-511	8

Chain E: 6 helices, 23 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	53-58	6	9
β-strand	63-71	9	9
β-strand	94-96	3	10
β-strand	98	1	9
β-strand	100	1	11
β-strand	103	1	11
β-strand	112-114	3	10
β-strand	121-129	9	9
β-strand	142-149	8	9
β-strand	155-160	6	9
β-strand	164-171	8	9
α-helix	181-182	2
α-helix	184-186	3
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	234-242	9	9
α-helix	244-247	4
α-helix	250-253	4
β-strand	262-266	5	9
α-helix	274-276	3

Chain G: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	14
β-strand	12-16	5	14
α-helix	17-18	2
β-strand	23-33	11	14
β-strand	36-46	11	14
β-strand	53-58	6	14
β-strand	63-71	9	14
β-strand	94-96	3	15
β-strand	98	1	14
β-strand	112-114	3	15
β-strand	121-129	9	14
β-strand	142-149	8	14
β-strand	155-160	6	14
β-strand	164-171	8	14
α-helix	181-182	2
α-helix	184-186	3
β-strand	189-196	8	16
β-strand	197-199	3	14
β-strand	200	1	17
β-strand	204	1	17
β-strand	207	1	18
β-strand	210	1	18
β-strand	211-216	6	16
β-strand	221-229	9	14
β-strand	234-242	9	14
α-helix	244-247	4
α-helix	250-253	4
β-strand	259-266	8	14

Chain I: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	19
β-strand	12-16	5	19
β-strand	23-31	9	19
α-helix	36-37	2
β-strand	38-46	9	19
β-strand	53-58	6	19
β-strand	63-71	9	19
β-strand	94-96	3	20
β-strand	98	1	19
α-helix	105-108	4
β-strand	112-114	3	20
α-helix	115	1
β-strand	121-129	9	19
β-strand	142-149	8	19
β-strand	155-160	6	19
β-strand	164-171	8	19
α-helix	181-182	2
α-helix	184-186	3
α-helix	188	1
β-strand	189-196	8	21
β-strand	197-199	3	19
β-strand	211-216	6	21
β-strand	221-228	8	19
β-strand	235-242	8	19
α-helix	244-247	4
α-helix	250-253	4
β-strand	259-266	8	19

Chain K: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	22
β-strand	12-16	5	22
β-strand	23-32	10	22
β-strand	37-46	10	22
β-strand	53-58	6	22
β-strand	63-71	9	22
β-strand	94-96	3	23
β-strand	98	1	22
β-strand	100	1	24
β-strand	103	1	24
α-helix	105-108	4
β-strand	112-114	3	23
β-strand	121-129	9	22
β-strand	142-149	8	22
β-strand	155-160	6	22
β-strand	164-171	8	22
α-helix	184-186	3
β-strand	189-196	8	25
β-strand	197-200	4	22
β-strand	204	1	22
β-strand	211-216	6	25
β-strand	221-227	7	22
β-strand	236-242	7	22
α-helix	244-247	4
α-helix	250-253	4
α-helix	254-256	3
β-strand	261-266	6	22

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Urokinase plasminogen activator surface receptor	A, C, E, G, I, K, M, O	protein	313	Homo sapiens	Q03405 (AlphaFold model)
antagonist peptide	B, D, F, H, J, L, N, P	protein	13

Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA

>1YWH_1 Urokinase plasminogen activator surface receptor (chains A, C, E, G, I, K, M, O)
LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTG
LKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEE
QCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGP
ILELENLPQNGRQCYSCKGQSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRG
CATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSGAAPQPGPAHLSLTITLL
MTARLWGGTLLWT

Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA

>1YWH_2 antagonist peptide (chains B, D, F, H, J, L, N, P)
KSDAFSKYLWSSK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal structure of the human urokinase plasminogen activator receptor bound to an antagonist peptide. Llinas, P., Le Du, M.H., Gardsvoll, H. et al. EMBO J (2005) 24:1655-1663. DOI 10.1038/sj.emboj.7600635 · 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
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
9YC6 4.8 Å, Mutant human uPAR bound to the Fab fragment of the targeted cancer therapeutic antibody…

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