3BT1 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF UROKINASE RECEPTOR, UROKINASE AND VITRONECTIN COMPLEX

Authors :   M. Huang

Date :   27 Dec 07 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,U
Biol. Unit 1: A,B,U  (1x)
Biol. Unit 2: A,U  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Protein-Protein Complex, Glycoprotein, Gpi-Anchor, Lipoprotein, Membrane, Receptor, Secreted, Blood Coagulation, Egf-Like Domain, Fibrinolysis, Hydrolase, Kringle, Phosphoprotein, Plasminogen Activation, Protease, Serine Protease, Zymogen, Cell Adhesion, Heparin-Binding, Sulfation, Immunoglobulin Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Huai, A. Zhou, L. Lin, A. P. Mazar, G. C. Parry, J. Callahan, D. E. Shaw B. Furie, B. C. Furie, M. Huang
Crystal Structures Of Two Human Vitronectin, Urokinase And Urokinase Receptor Complexes
Nat. Struct. Mol. Biol. V. 15 422 2008
PubMed-ID: 18376415 | Reference-DOI: 10.1038/NSMB.1404

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PMT/BIP
	Expression System Strain	:	S2 CELLS
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	UROKINASE AMINO TERMINAL FRAGMENT, UROKINASE-TYPE PLASMINOGEN ACTIVATOR LONG CHAIN A, UNP RESIDUES 21-153
	Gene	:	PLAU
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UPA, U-PLASMINOGEN ACTIVATOR

Molecule 2 - VITRONECTIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	SOMETOMEDIN-B DOMAIN
	Gene	:	VTN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SERUM-SPREADING FACTOR, S-PROTEIN, V75

Molecule 3 - UROKINASE PLASMINOGEN ACTIVATOR SURFACE RECEPTOR
	Chains	:	U
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PMT/BIP
	Expression System Strain	:	S2 CELLS
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Gene	:	PLAUR, MO3, UPAR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UPAR, U-PAR, MONOCYTE ACTIVATION ANTIGEN MO3, CD87 ANTIGEN

		1	2	3
Asymmetric Unit	:	A	B	U
Biological Unit 1 (1x)	:	A	B	U
Biological Unit 2 (1x)	:	A		U
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN U:52	BINDING SITE FOR RESIDUE NAG U 1052
2	AC2	SOFTWARE	MET A:67 , MET A:127 , ASN U:172	BINDING SITE FOR RESIDUE NAG U 1172
3	AC3	SOFTWARE	ASN U:200 , THR U:202 , HIS U:203	BINDING SITE FOR RESIDUE NAG U 1200
4	AC4	SOFTWARE	HIS U:203	BINDING SITE FOR RESIDUE NAG U 1201
5	AC5	SOFTWARE	GLU B:23	BINDING SITE FOR RESIDUE MAN U 1202

Asymmetric Unit

No.	Residues
1	A:11	-	A:19
2	A:13	-	A:31
3	A:33	-	A:42
4	A:50	-	A:131
5	A:71	-	A:113
6	A:102	-	A:126
7	B:5	-	B:32
8	B:5	-	B:21
9	B:9	-	B:39
10	B:19	-	B:32
11	B:25	-	B:31
12	U:3	-	U:24
13	U:3	-	U:17
14	U:6	-	U:12
15	U:17	-	U:45
16	U:71	-	U:76
17	U:95	-	U:122
18	U:98	-	U:105
19	U:115	-	U:147
20	U:153	-	U:170
21	U:171	-	U:176
22	U:194	-	U:222
23	U:197	-	U:205
24	U:215	-	U:241
25	U:247	-	U:265
26	U:266	-	U:271

(no "Cis Peptide Bond" information available for 3BT1)

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016322	E	55	G	UPAR_HUMAN	Polymorphism	4251813	U	E	33	G
2	UniProt	VAR_016323	T	86	A	UPAR_HUMAN	Polymorphism	399145	U	T	64	A
3	UniProt	VAR_006722	P	141	L	UROK_HUMAN	Polymorphism	2227564	A	P	121	L
4	UniProt	VAR_016325	K	220	R	UPAR_HUMAN	Polymorphism	2302524	U	K	198	R
5	UniProt	VAR_016326	N	281	K	UPAR_HUMAN	Polymorphism	4251921	U	N	259	K
6	UniProt	VAR_052698	D	297	A	UPAR_HUMAN	Polymorphism	16976608	U	D	275	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016322	E	55	G	UPAR_HUMAN	Polymorphism	4251813	U	E	33	G
2	UniProt	VAR_016323	T	86	A	UPAR_HUMAN	Polymorphism	399145	U	T	64	A
3	UniProt	VAR_006722	P	141	L	UROK_HUMAN	Polymorphism	2227564	A	P	121	L
4	UniProt	VAR_016325	K	220	R	UPAR_HUMAN	Polymorphism	2302524	U	K	198	R
5	UniProt	VAR_016326	N	281	K	UPAR_HUMAN	Polymorphism	4251921	U	N	259	K
6	UniProt	VAR_052698	D	297	A	UPAR_HUMAN	Polymorphism	16976608	U	D	275	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016322	E	55	G	UPAR_HUMAN	Polymorphism	4251813	U	E	33	G
2	UniProt	VAR_016323	T	86	A	UPAR_HUMAN	Polymorphism	399145	U	T	64	A
3	UniProt	VAR_006722	P	141	L	UROK_HUMAN	Polymorphism	2227564	A	P	121	L
4	UniProt	VAR_016325	K	220	R	UPAR_HUMAN	Polymorphism	2302524	U	K	198	R
5	UniProt	VAR_016326	N	281	K	UPAR_HUMAN	Polymorphism	4251921	U	N	259	K
6	UniProt	VAR_052698	D	297	A	UPAR_HUMAN	Polymorphism	16976608	U	D	275	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (5, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LY6_UPAR	PS00983	Ly-6 / u-PAR domain signature.	UPAR_HUMAN	24-67 116-169 215-269	3	U:2-45 U:94-147 U:193-247
2	SMB_1	PS00524	Somatomedin B domain (SMB) signature.	VTNC_HUMAN	38-58	1	B:19-39
3	EGF_1	PS00022	EGF-like domain signature 1.	UROK_HUMAN	51-62	1	A:31-42
4	KRINGLE_2	PS50070	Kringle domain profile.	UROK_HUMAN	69-151	1	A:49-131
5	KRINGLE_1	PS00021	Kringle domain signature.	UROK_HUMAN	121-133	1	A:101-113

Biological Unit 1 (5, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LY6_UPAR	PS00983	Ly-6 / u-PAR domain signature.	UPAR_HUMAN	24-67 116-169 215-269	3	U:2-45 U:94-147 U:193-247
2	SMB_1	PS00524	Somatomedin B domain (SMB) signature.	VTNC_HUMAN	38-58	1	B:19-39
3	EGF_1	PS00022	EGF-like domain signature 1.	UROK_HUMAN	51-62	1	A:31-42
4	KRINGLE_2	PS50070	Kringle domain profile.	UROK_HUMAN	69-151	1	A:49-131
5	KRINGLE_1	PS00021	Kringle domain signature.	UROK_HUMAN	121-133	1	A:101-113

Biological Unit 2 (4, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LY6_UPAR	PS00983	Ly-6 / u-PAR domain signature.	UPAR_HUMAN	24-67 116-169 215-269	3	U:2-45 U:94-147 U:193-247
2	SMB_1	PS00524	Somatomedin B domain (SMB) signature.	VTNC_HUMAN	38-58	0	-
3	EGF_1	PS00022	EGF-like domain signature 1.	UROK_HUMAN	51-62	1	A:31-42
4	KRINGLE_2	PS50070	Kringle domain profile.	UROK_HUMAN	69-151	1	A:49-131
5	KRINGLE_1	PS00021	Kringle domain signature.	UROK_HUMAN	121-133	1	A:101-113

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LY6_UPAR	PS00983	Ly-6 / u-PAR domain signature.	UPAR_HUMAN	24-67 116-169 215-269	0	- - -
2	SMB_1	PS00524	Somatomedin B domain (SMB) signature.	VTNC_HUMAN	38-58	1	B:19-39
3	EGF_1	PS00022	EGF-like domain signature 1.	UROK_HUMAN	51-62	0	-
4	KRINGLE_2	PS50070	Kringle domain profile.	UROK_HUMAN	69-151	0	-
5	KRINGLE_1	PS00021	Kringle domain signature.	UROK_HUMAN	121-133	0	-

Asymmetric Unit (12, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000226218	1	ENSE00001177296	chr17:26697717-26697161	557	VTNC_HUMAN	1-22	22	1	B:2-3	2
1.2	ENST00000226218	2	ENSE00000705689	chr17:26697067-26696948	120	VTNC_HUMAN	22-62	41	1	B:3-41	39
1.3	ENST00000226218	3	ENSE00000866275	chr17:26696872-26696528	345	VTNC_HUMAN	62-177	116	0	-	-
1.4	ENST00000226218	4	ENSE00000866274	chr17:26696449-26696310	140	VTNC_HUMAN	177-223	47	0	-	-
1.5	ENST00000226218	5	ENSE00000705693	chr17:26696049-26695893	157	VTNC_HUMAN	224-276	53	0	-	-
1.6	ENST00000226218	6	ENSE00000705695	chr17:26695694-26695542	153	VTNC_HUMAN	276-327	52	0	-	-
1.7a	ENST00000226218	7a	ENSE00000705697	chr17:26695080-26694736	345	VTNC_HUMAN	327-442	116	0	-	-
1.8b	ENST00000226218	8b	ENSE00001177290	chr17:26694502-26694297	206	VTNC_HUMAN	442-478	37	0	-	-

2.1	ENST00000340093	1	ENSE00001048170	chr19:44174502-44174218	285	UPAR_HUMAN	1-19	19	0	-	-
2.2	ENST00000340093	2	ENSE00000847438	chr19:44171843-44171733	111	UPAR_HUMAN	19-56	38	1	U:1-34	34
2.3	ENST00000340093	3	ENSE00000494759	chr19:44169611-44169468	144	UPAR_HUMAN	56-104	49	1	U:34-82	49
2.4	ENST00000340093	4	ENSE00000710867	chr19:44160792-44160631	162	UPAR_HUMAN	104-158	55	1	U:82-136 (gaps)	55
2.5	ENST00000340093	5	ENSE00000710856	chr19:44159725-44159591	135	UPAR_HUMAN	158-203	46	1	U:136-181	46
2.6	ENST00000340093	6	ENSE00000847435	chr19:44156523-44156377	147	UPAR_HUMAN	203-252	50	1	U:181-230	50
2.7	ENST00000340093	7	ENSE00000847434	chr19:44153295-44152732	564	UPAR_HUMAN	252-335	84	1	U:230-275	46

3.3c	ENST00000372764	3c	ENSE00001820360	chr10:75670915-75670976	62	UROK_HUMAN	-	0	0	-	-
3.4b	ENST00000372764	4b	ENSE00002193721	chr10:75671283-75671370	88	UROK_HUMAN	1-19	19	0	-	-
3.5	ENST00000372764	5	ENSE00001276413	chr10:75671799-75671826	28	UROK_HUMAN	20-29	10	1	A:8-9	2
3.6a	ENST00000372764	6a	ENSE00001169210	chr10:75671973-75672080	108	UROK_HUMAN	29-65	37	1	A:9-45	37
3.7b	ENST00000372764	7b	ENSE00001169200	chr10:75672682-75672856	175	UROK_HUMAN	65-123	59	1	A:45-103	59
3.8	ENST00000372764	8	ENSE00000834105	chr10:75673048-75673139	92	UROK_HUMAN	123-154	32	1	A:103-132	30
3.9b	ENST00000372764	9b	ENSE00001169184	chr10:75673297-75673516	220	UROK_HUMAN	154-227	74	0	-	-
3.10	ENST00000372764	10	ENSE00001169178	chr10:75673738-75673886	149	UROK_HUMAN	227-277	51	0	-	-
3.11	ENST00000372764	11	ENSE00001169173	chr10:75674534-75674674	141	UROK_HUMAN	277-324	48	0	-	-
3.13	ENST00000372764	13	ENSE00001169164	chr10:75675009-75675157	149	UROK_HUMAN	324-373	50	0	-	-
3.14d	ENST00000372764	14d	ENSE00001892698	chr10:75676147-75677255	1109	UROK_HUMAN	374-431	58	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:125
 aligned with UROK_HUMAN | P00749 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:125
                                    37        47        57        67        77        87        97       107       117       127       137       147     
           UROK_HUMAN    28 PSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCA 152
               SCOP domains d3bt1a1 A:8-49                            d3bt1a2 A:50-132 Urokinase-type plasminogen activator                               SCOP domains
               CATH domains 3bt1A01 A:8-49 Laminin                    3bt1A02 A:50-132 Plasminogen Kringle 4                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee.......eeee....ee.....ee....ee..........................hhhhh.....hhhhhh..................eeee......eeee...ee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------L----------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------KRINGLE_2  PDB: A:49-131 UniProt: 69-151                                           - PROSITE (2)
                PROSITE (3) -----------------------EGF_1       ----------------------------------------------------------KRINGLE_1    ------------------- PROSITE (3)
           Transcript 3 (1) 3.-----------------------------------Exon 3.7b  PDB: A:45-103 UniProt: 65-123                   ----------------------------- Transcript 3 (1)
           Transcript 3 (2) -Exon 3.6a  PDB: A:9-45 UniProt: 29-65---------------------------------------------------------Exon 3.8  PDB: A:103-132       Transcript 3 (2)
                 3bt1 A   8 PSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCA 132
                                    17        27        37        47        57        67        77        87        97       107       117       127

Chain B from PDB  Type:PROTEIN  Length:40
 aligned with VTNC_HUMAN | P04004 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:40
                                    30        40        50        60
           VTNC_HUMAN    21 QESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKP  60
               SCOP domains d3bt1b_ B: Vitronectin                   SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------SMB_1  PDB: B:19-39  -- PROSITE (2)
           Transcript 1 (1) 1.-------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2  PDB: B:3-41 UniProt: 22-62    Transcript 1 (2)
                 3bt1 B   2 QESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKP  41
                                    11        21        31        41

Chain U from PDB  Type:PROTEIN  Length:273
 aligned with UPAR_HUMAN | Q03405 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:275
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     
           UPAR_HUMAN    23 LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPD 297
               SCOP domains d3bt1u1 U:1-86 Urokinase plasminogen activator surface receptor uPAR                  d3bt1u3 U:87-187 Urokinase plasminogen activator surface receptor uPAR                               d3bt1u2 U:188-275 Urokinase plasminogen activator surface receptor uPAR                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee......eeeeeeeeeee..eeeeeeeeeee.........eeee..eeeeeeeeee...........--.........eeeeee.hhh.......eeee......eeeeeeeee.............eeeeee......eeeeeee..eeeeeeee.................eeeeeeee.........hhhhheeeeee....eeeeeeeee.......eeeeee........hhhhhh.eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------G------------------------------A-------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------K---------------A SAPs(SNPs)
                    PROSITE -LY6_UPAR  PDB: U:2-45 UniProt: 24-67        ------------------------------------------------LY6_UPAR  PDB: U:94-147 UniProt: 116-169              ---------------------------------------------LY6_UPAR  PDB: U:193-247 UniProt: 215-269              ---------------------------- PROSITE
           Transcript 2 (1) Exon 2.2  PDB: U:1-34 [INCOMPLETE]-----------------------------------------------Exon 2.4  PDB: U:82-136 (gaps) UniProt: 104-158        --------------------------------------------Exon 2.6  PDB: U:181-230 UniProt: 203-252         --------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) ---------------------------------Exon 2.3  PDB: U:34-82 UniProt: 56-104           -----------------------------------------------------Exon 2.5  PDB: U:136-181 UniProt: 158-203     ------------------------------------------------Exon 2.7  PDB: U:230-275 UniProt: 252-335      Transcript 2 (2)
                 3bt1 U   1 LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSG--VTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPD 275
                                    10        20        30        40        50        60        70        80 |  |   90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     
                                                                                                            82 85

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Plasminogen Kringle 4 (42)

Homologous Superfamily: Plasminogen Kringle 4 (42)

Human (Homo sapiens) (37)

3bt1A02

A:50-132

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

Human (Homo sapiens) (195)

3bt1A01

A:8-49

(no "Pfam Domain" information available for 3BT1)

Asymmetric Unit(hide GO term definitions)

Chain A (UROK_HUMAN | P00749)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0071498	cellular response to fluid shear stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
	GO:0071333	cellular response to glucose stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
	GO:0035729	cellular response to hepatocyte growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus.
	GO:0071456	cellular response to hypoxia	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0071310	cellular response to organic substance	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0072734	cellular response to staurosporine	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a staurosporine stimulus.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0007566	embryo implantation	Attachment of the blastocyst to the uterine lining.
	GO:0042730	fibrinolysis	A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0070997	neuron death	The process of cell death in a neuron.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0060279	positive regulation of ovulation	Any process that activates or increases the frequency, rate or extent of ovulation, the release of a mature ovum/oocyte from an ovary.
	GO:2000379	positive regulation of reactive oxygen species metabolic process	Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
	GO:0014911	positive regulation of smooth muscle cell migration	Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0033628	regulation of cell adhesion mediated by integrin	Any process that modulates the frequency, rate, or extent of cell adhesion mediated by integrin.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:2000345	regulation of hepatocyte proliferation	Any process that modulates the frequency, rate or extent of hepatocyte proliferation.
	GO:0010469	regulation of receptor activity	Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0014910	regulation of smooth muscle cell migration	Any process that modulates the frequency, rate or extent of smooth muscle cell migration.
	GO:2000097	regulation of smooth muscle cell-matrix adhesion	Any process that modulates the frequency, rate or extent of smooth muscle cell-matrix adhesion.
	GO:0061041	regulation of wound healing	Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
	GO:0014823	response to activity	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an activity stimulus.
	GO:0035728	response to hepatocyte growth factor	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus.
	GO:0055093	response to hyperoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating increased oxygen tension.
	GO:0001666	response to hypoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0043403	skeletal muscle tissue regeneration	The regrowth of skeletal muscle tissue to repair injured or damaged muscle fibers in the postnatal stage.
	GO:0014909	smooth muscle cell migration	The orderly movement of a smooth muscle cell from one site to another, often during the development of a multicellular organism.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B (VTNC_HUMAN | P04004)

molecular function
	GO:0050840	extracellular matrix binding	Interacting selectively and non-covalently with a component of the extracellular matrix.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0005178	integrin binding	Interacting selectively and non-covalently with an integrin.
	GO:0030247	polysaccharide binding	Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005044	scavenger receptor activity	Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs).
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0033627	cell adhesion mediated by integrin	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits.
	GO:0007160	cell-matrix adhesion	The binding of a cell to the extracellular matrix via adhesion molecules.
	GO:0035987	endodermal cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0030195	negative regulation of blood coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0048709	oligodendrocyte differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
	GO:0010811	positive regulation of cell-substrate adhesion	Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0032092	positive regulation of protein binding	Any process that activates or increases the frequency, rate or extent of protein binding.
	GO:0048260	positive regulation of receptor-mediated endocytosis	Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
	GO:0014911	positive regulation of smooth muscle cell migration	Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
	GO:0030949	positive regulation of vascular endothelial growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
	GO:0090303	positive regulation of wound healing	Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:0030449	regulation of complement activation	Any process that modulates the frequency, rate or extent of complement activation.
	GO:0061302	smooth muscle cell-matrix adhesion	The binding of a smooth muscle cell to the extracellular matrix via adhesion molecules.
cellular component
	GO:0071062	alphav-beta3 integrin-vitronectin complex	A protein complex that consists of an alphav-beta3 integrin complex bound to vitronectin.
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Chain U (UPAR_HUMAN | Q03405)

molecular function
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0030377	urokinase plasminogen activator receptor activity	Combining with the urokinase plasminogen activator to initiate a change in cell activity.
biological process
	GO:0016255	attachment of GPI anchor to protein	A transamidation reaction that results in the cleavage of the polypeptide chain and the concomitant transfer of the GPI anchor to the newly formed carboxy-terminal amino acid of the anchored protein. The cleaved C-terminal contains the C-terminal GPI signal sequence of the newly synthesized polypeptide chain.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0042730	fibrinolysis	A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
	GO:0006928	movement of cell or subcellular component	The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:2001268	negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of cysteine-type endopeptidase activity involved in apoptotic signaling pathway.
	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:0043388	positive regulation of DNA binding	Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
	GO:0045742	positive regulation of epidermal growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:0090200	positive regulation of release of cytochrome c from mitochondria	Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
	GO:0030162	regulation of proteolysis	Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0038195	urokinase plasminogen activator signaling pathway	A series of molecular signals initiated by the binding of urokinase plasminogen activator to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0071438	invadopodium membrane	The portion of the plasma membrane surrounding an invadopodium.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	3bt1
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	UPAR_HUMAN \| Q03405
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	UROK_HUMAN \| P00749
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	VTNC_HUMAN \| P04004
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2fd6	STRUCTURE OF UROKINASE RECEPTOR IN COMPLEX WITH UROKINASE
3bt2	THE SAME PROTEIN COMPLEX WITH FAB FRAGMENTS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (26, 26)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (6, 6)

PROSITE Motifs (5, 7)

Exons (12, 12)

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