3BT1: Urokinase-type plasminogen activator

Structure of urokinase receptor, urokinase and vitronectin complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Mar 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,461
Mol. weight: 52.56 kDa
Ligands: NAG
Released: 25 Mar 2008

Explore 3BT1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BT1 contains 11 α-helices and 38 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18-21	4	1
β-strand	29-32	4	1
β-strand	37-38	2	2
β-strand	44-45	2	2
β-strand	50-51	2	3
β-strand	64	1	4
β-strand	65	1	5
α-helix	69	1
β-strand	70	1	4
α-helix	71-73	3
α-helix	79-81	3
α-helix	89-92	4
β-strand	103	1	6
β-strand	112-115	4	6
β-strand	122-125	4	6
β-strand	126	1	5
β-strand	129-130	2	3

Chain B: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	7
α-helix	25-28	4
β-strand	31	1	7
α-helix	35-38	4

Chain U: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	12-16	5	8
β-strand	23-33	11	8
β-strand	36-46	11	8
β-strand	53	1	8
β-strand	56-59	4	8
β-strand	62-71	10	8
β-strand	94-97	4	9
β-strand	98-99	2	8
α-helix	100-102	3
β-strand	111-114	4	9
β-strand	121-129	9	8
β-strand	140	1	1
β-strand	143-148	6	8
β-strand	155-161	7	8
β-strand	164-171	8	8
α-helix	181-182	2
α-helix	188	1
β-strand	189-196	8	10
β-strand	197	1	8
β-strand	200	1	11
β-strand	204	1	11
α-helix	207-209	3
β-strand	211-216	6	10
β-strand	221-229	9	8
β-strand	237-242	6	8
α-helix	252-255	4
β-strand	258-266	9	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Urokinase-type plasminogen activator	A	protein	135	Homo sapiens	P00749 (AlphaFold model)
Vitronectin	B	protein	40	Homo sapiens	P04004 (AlphaFold model)
Urokinase plasminogen activator surface receptor	U	protein	283	Homo sapiens	Q03405 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3BT1_1 Urokinase-type plasminogen activator (chains A)
RSSNELHQVPSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFY
RGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVG
LKPLVQECMVHDCAD

Sequence of entity 2 (B), FASTA

>3BT1_2 Vitronectin (chains B)
QESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKP

Sequence of entity 3 (U), FASTA

>3BT1_3 Urokinase plasminogen activator surface receptor (chains U)
RSLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYR
TGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSP
EEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNE
GPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMV
RGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYR

Ligands and cofactors

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

Primary citation

Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes. Huai, Q., Zhou, A., Lin, L. et al. Nat Struct Mol Biol (2008) 15:422-423. DOI 10.1038/nsmb.1404 · PubMed

Other PDB entries of the same protein (UniProt P00749 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YC6 1.18 Å, The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH4.6
4ZKO 1.29 Å, The crystal structure of upain-1-W3A in complex with uPA at pH7.4
4ZKN 1.36 Å, The crystal structure of upain-1-W3A in complex with uPA at pH5.5
4ZKR 1.36 Å, The crystal structure of upain-1-W3A in complex with uPA at pH9.0
6XVD 1.4 Å, Crystal structure of complex of urokinase and a upain-1 variant(W3F) in pH7.4 condition
2O8T 1.45 Å, Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator…
3MHW 1.45 Å, The complex crystal Structure of Urokianse and 2-Aminobenzothiazole
5Z1C 1.45 Å, The crystal structure of uPA in complex with 4-Iodobenzylamine at pH7.4
5WXF 1.46 Å, Crystal structure of uPA in complex with upain-2-2
4MNW 1.49 Å, Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic…
1GJ7 1.5 Å, Engineering inhibitors highly selective for the S1 sites of SER190 trypsin-like serine…
4XSK 1.5 Å, Structure of PAItrap, an uPA mutant

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