2FD6: Human Urokinase Plasminogen Activator

Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A. Determined by X-ray diffraction at 1.9 Å resolution. Released 21 Feb 2006.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 6,600
Mol. weight: 92.83 kDa
Ligands: NDG, ETX
Released: 21 Feb 2006

Explore 2FD6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2FD6 contains 24 α-helices and 81 β-strands across 4 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: 3 helices, 14 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	51	1	3
β-strand	64	1	4
β-strand	65	1	5
β-strand	70	1	4
β-strand	71	1	6
α-helix	72-73	2
α-helix	79-81	3
α-helix	91-94	4
β-strand	103	1	6
β-strand	112-117	6	6
β-strand	120-125	6	6
β-strand	126	1	5
β-strand	130	1	3

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	46-52	7	13
β-strand	53-59	7	13
α-helix	61-63	3
β-strand	67-72	6	12
α-helix	73-75	3
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	100A-103	4	13
β-strand	107-111	5	13
β-strand	117	1	14
β-strand	120-122	3	15
β-strand	130-131	2	16
β-strand	136-140	5	15
β-strand	141	1	14
β-strand	146-149	4	17
α-helix	150-152	3
β-strand	154	1	17
β-strand	158-160	3	18
α-helix	161-163	3
β-strand	164-166	3	15
β-strand	169-173	5	15
β-strand	174-176	3	18
β-strand	178-179	2	16
β-strand	189-194	6	17
α-helix	195-197	3
β-strand	199-204	6	17

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	97	1
β-strand	98	1	8
α-helix	99	1
β-strand	102-106	5	8
β-strand	110	1	9
β-strand	113-117	5	10
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	10
β-strand	139	1	9
β-strand	144-149	6	11
β-strand	152-154	3	11
β-strand	158-162	5	10
α-helix	163-166	4
β-strand	172-181	10	10
α-helix	182-186	5
β-strand	190-196	7	11
β-strand	204-209	6	11

Chain U: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	19
β-strand	12-16	5	19
α-helix	17-18	2
β-strand	23-32	10	19
β-strand	38-46	9	19
β-strand	53-59	7	19
β-strand	62-71	10	19
β-strand	94-97	4	20
β-strand	98-99	2	19
β-strand	111-114	4	20
β-strand	121-128	8	19
β-strand	143-149	7	19
β-strand	155-161	7	19
β-strand	164-171	8	19
α-helix	181-182	2
α-helix	184-186	3
β-strand	189-196	8	21
β-strand	197-199	3	19
β-strand	200	1	22
β-strand	204	1	22
β-strand	211-216	6	21
β-strand	221-229	9	19
β-strand	234-242	9	19
α-helix	244-246	3
α-helix	253-256	4
β-strand	262-266	5	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Urokinase-type plasminogen activator	A	protein	122	Homo sapiens	P00749 (AlphaFold model)
L chain of Fab of ATN-615 anti-uPAR antibody	L	protein	214	Mus musculus	P01837 (AlphaFold model)
H chain of Fab of ATN-615 anti-uPAR antibody	H	protein	213	Mus musculus	P01868 (AlphaFold model)
Urokinase plasminogen activator surface receptor	U	protein	276	Homo sapiens	Q03405 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2FD6_1 Urokinase-type plasminogen activator (chains A)
CDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFYRGKASTDTMGRP
CLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVGLKPLVQECMVHD
CA

Sequence of entity 2 (L), FASTA

>2FD6_2 L chain of Fab of ATN-615 anti-uPAR antibody (chains L)
DIVLTQSPDITAASLGQKVTITCSASSSVSYMHWYQQKSGTSPKPWIFEISKLASGVPAR
FSGSGSGTSYSLTISSMEAEDAAIYYCQQWNYPFTFGGGTKLEIKRADAAPTVSIFPPSS
EQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLT
KDEYERHNSYTCEATHKTSTSPIVKSFNRNEAKA

Sequence of entity 3 (H), FASTA

>2FD6_3 H chain of Fab of ATN-615 anti-uPAR antibody (chains H)
GVKLQQSGPEVVKPGASVKISCKASGYSFTNFYIHWVKQRPGQGLEWIGWIFHGSDNTEY
NEKFKDKATLTADTSSSTAYMQLSSLTSEDSAVYFCARWGPHWYFDVWGQGTTVTVSSAK
TTPPSVYPLAPGNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVPSSTWPSETVTCNVAHPASSTKVDKKIAAA

Sequence of entity 4 (U), FASTA

>2FD6_4 Urokinase plasminogen activator surface receptor (chains U)
SLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRT
GLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPE
EQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEG
PILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVR
GCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPD

Ligands and cofactors

ID	Name	Formula	Copies
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	C8 H15 N O6	1
ETX	2-ethoxyethanol	C4 H10 O2	3

Water and common crystallization additives (EDO, PGE, SO4, PG4) are not listed.

Primary citation

Structure of human urokinase plasminogen activator in complex with its receptor. Huai, Q., Mazar, A.P., Kuo, A. et al. Science (2006) 311:656-659. DOI 10.1126/science.1121143 · 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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