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(-) Description

Title :  STRUCTURE OF HUMAN UROKINASE PLASMINOGEN ACTIVATOR IN COMPLEX WITH UROKINASE RECEPTOR AND AN ANTI-UPAR ANTIBODY AT 1.9 A
 
Authors :  M. Huang, Q. Huai, Y. Li
Date :  13 Dec 05  (Deposition) - 21 Feb 06  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,H,L,U
Biol. Unit 1:  A,H,L,U  (1x)
Biol. Unit 2:  A (1x),H (1x),L (1x),U (1x)
Keywords :  Upar, Atf, Atn-615 Antibody, Fab, Ternary Complex, Immune System, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Huai, A. P. Mazar, A. Kuo, G. C. Parry, D. E. Shaw, J. Callahan, Y. Li, C. Yuan, C. Bian, L. Chen, B. Furie, B. C. Furie, D. B. Cines, M. Huang
Structure Of Human Urokinase Plasminogen Activator In Complex With Its Receptor
Science V. 311 656 2006
PubMed-ID: 16456079  |  Reference-DOI: 10.1126/SCIENCE.1121143

(-) Compounds

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
    ChainsA
    EC Number3.4.21.73
    EngineeredYES
    Expression SystemDROSOPHILA
    Expression System Cell LineS2 CELLS
    Expression System CommonFRUIT FLIES
    Expression System Taxid7215
    Expression System VectorPMT-BIP-V5-HIS
    FragmentAMINO TERMINAL RESIDUES 31-152
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - L CHAIN OF FAB OF ATN-615 ANTI-UPAR ANTIBODY
    ChainsL
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SecretionASCITE LIQUID
 
Molecule 3 - H CHAIN OF FAB OF ATN-615 ANTI-UPAR ANTIBODY
    ChainsH
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SecretionASCITE LIQUID
 
Molecule 4 - UROKINASE PLASMINOGEN ACTIVATOR SURFACE RECEPTOR
    ChainsU
    EngineeredYES
    Expression SystemDROSOPHILA
    Expression System Cell LineS2 CELLS
    Expression System CommonFRUIT FLIES
    Expression System Taxid7215
    Expression System VectorPMT-BIP-V5-HIS
    FragmentRESIDUES 23-297
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUPAR, U-PAR, MONOCYTE ACTIVATION ANTIGEN MO3, CD87 ANTIGEN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit AHLU
Biological Unit 1 (1x)AHLU
Biological Unit 2 (1x)A (1x)H (1x)L (1x)U (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 13)

Asymmetric Unit (8, 13)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ETX3Ligand/Ion2-ETHOXYETHANOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6PG41Ligand/IonTETRAETHYLENE GLYCOL
7PGE1Ligand/IonTRIETHYLENE GLYCOL
8SO41Ligand/IonSULFATE ION
Biological Unit 1 (8, 13)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ETX3Ligand/Ion2-ETHOXYETHANOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6PG41Ligand/IonTETRAETHYLENE GLYCOL
7PGE1Ligand/IonTRIETHYLENE GLYCOL
8SO41Ligand/IonSULFATE ION
Biological Unit 2 (5, 7)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2ETX-1Ligand/Ion2-ETHOXYETHANOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6PG41Ligand/IonTETRAETHYLENE GLYCOL
7PGE-1Ligand/IonTRIETHYLENE GLYCOL
8SO41Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:12 , HIS A:29 , HIS A:41 , HOH A:511 , HOH A:523 , HOH U:501BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREASP L:1 , ILE L:2 , GLN L:90 , ASN L:92 , PRO L:94 , HOH L:444BINDING SITE FOR RESIDUE ETX L 401
03AC3SOFTWAREPRO L:46 , SER L:56BINDING SITE FOR RESIDUE EDO L 405
04AC4SOFTWARETYR L:93 , HOH L:489 , GLY U:191 , GLN U:193BINDING SITE FOR RESIDUE ETX L 407
05AC5SOFTWARELYS H:23 , SER H:75 , THR H:77 , HOH H:410 , HOH H:427BINDING SITE FOR RESIDUE ETX H 403
06AC6SOFTWARELYS H:19 , THR H:70 , ALA H:71BINDING SITE FOR RESIDUE EDO H 404
07AC7SOFTWAREASN H:31 , PHE H:32 , TYR H:33 , TRP H:95 , TRP H:99 , LEU U:187 , PRO U:218 , PG4 U:402BINDING SITE FOR RESIDUE PGE H 406
08AC8SOFTWAREASN U:52 , VAL U:70 , FUC U:453 , HOH U:530BINDING SITE FOR RESIDUE NAG U 452
09AC9SOFTWARENAG U:452BINDING SITE FOR RESIDUE FUC U 453
10BC1SOFTWAREASN U:172 , NAG U:473BINDING SITE FOR RESIDUE NAG U 472
11BC2SOFTWARENAG U:472BINDING SITE FOR RESIDUE NAG U 473
12BC3SOFTWAREASN U:200 , THR U:202 , HIS U:203BINDING SITE FOR RESIDUE NDG U 400
13BC4SOFTWAREASN H:31 , PHE H:52 , HIS H:52A , ASN H:56 , PGE H:406 , PRO U:218 , ASN U:220 , GLN U:221 , THR U:243 , ALA U:244 , HOH U:475 , HOH U:486BINDING SITE FOR RESIDUE PG4 U 402

(-) SS Bonds  (23, 23)

Asymmetric Unit
No.Residues
1A:13 -A:31
2A:33 -A:42
3A:50 -A:131
4A:71 -A:113
5A:102 -A:126
6H:22 -H:92
7H:135 -H:190
8L:23 -L:88
9L:133 -L:193
10U:3 -U:24
11U:6 -U:12
12U:17 -U:45
13U:71 -U:76
14U:95 -U:122
15U:98 -U:105
16U:115 -U:147
17U:153 -U:170
18U:171 -U:176
19U:194 -U:222
20U:197 -U:205
21U:215 -U:241
22U:247 -U:265
23U:266 -U:271

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:139 -Pro L:140
3Phe H:141 -Pro H:142
4Glu H:143 -Pro H:144
5Trp H:183 -Pro H:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016322E55GUPAR_HUMANPolymorphism4251813UE33G
2UniProtVAR_016323T86AUPAR_HUMANPolymorphism399145UT64A
3UniProtVAR_006722P141LUROK_HUMANPolymorphism2227564AP121L
4UniProtVAR_016325K220RUPAR_HUMANPolymorphism2302524UK198R
5UniProtVAR_016326N281KUPAR_HUMANPolymorphism4251921UN259K
6UniProtVAR_052698D297AUPAR_HUMANPolymorphism16976608UD275A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016322E55GUPAR_HUMANPolymorphism4251813UE33G
2UniProtVAR_016323T86AUPAR_HUMANPolymorphism399145UT64A
3UniProtVAR_006722P141LUROK_HUMANPolymorphism2227564AP121L
4UniProtVAR_016325K220RUPAR_HUMANPolymorphism2302524UK198R
5UniProtVAR_016326N281KUPAR_HUMANPolymorphism4251921UN259K
6UniProtVAR_052698D297AUPAR_HUMANPolymorphism16976608UD275A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016322E55GUPAR_HUMANPolymorphism4251813UE33G
2UniProtVAR_016323T86AUPAR_HUMANPolymorphism399145UT64A
3UniProtVAR_006722P141LUROK_HUMANPolymorphism2227564AP121L
4UniProtVAR_016325K220RUPAR_HUMANPolymorphism2302524UK198R
5UniProtVAR_016326N281KUPAR_HUMANPolymorphism4251921UN259K
6UniProtVAR_052698D297AUPAR_HUMANPolymorphism16976608UD275A

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

(-) PROSITE Motifs  (4, 6)

Asymmetric Unit (4, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LY6_UPARPS00983 Ly-6 / u-PAR domain signature.UPAR_HUMAN24-67
116-169
215-269
  3U:2-45
U:94-147
U:193-247
2EGF_1PS00022 EGF-like domain signature 1.UROK_HUMAN51-62  1A:31-42
3KRINGLE_2PS50070 Kringle domain profile.UROK_HUMAN69-151  1A:49-131
4KRINGLE_1PS00021 Kringle domain signature.UROK_HUMAN121-133  1A:101-113
Biological Unit 1 (4, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LY6_UPARPS00983 Ly-6 / u-PAR domain signature.UPAR_HUMAN24-67
116-169
215-269
  3U:2-45
U:94-147
U:193-247
2EGF_1PS00022 EGF-like domain signature 1.UROK_HUMAN51-62  1A:31-42
3KRINGLE_2PS50070 Kringle domain profile.UROK_HUMAN69-151  1A:49-131
4KRINGLE_1PS00021 Kringle domain signature.UROK_HUMAN121-133  1A:101-113
Biological Unit 2 (4, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LY6_UPARPS00983 Ly-6 / u-PAR domain signature.UPAR_HUMAN24-67
116-169
215-269
  3U:2-45
U:94-147
U:193-247
2EGF_1PS00022 EGF-like domain signature 1.UROK_HUMAN51-62  1A:31-42
3KRINGLE_2PS50070 Kringle domain profile.UROK_HUMAN69-151  1A:49-131
4KRINGLE_1PS00021 Kringle domain signature.UROK_HUMAN121-133  1A:101-113

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003400931ENSE00001048170chr19:44174502-44174218285UPAR_HUMAN1-19190--
1.2ENST000003400932ENSE00000847438chr19:44171843-44171733111UPAR_HUMAN19-56381U:1A-3334
1.3ENST000003400933ENSE00000494759chr19:44169611-44169468144UPAR_HUMAN56-104491U:37-8044
1.4ENST000003400934ENSE00000710867chr19:44160792-44160631162UPAR_HUMAN104-158551U:92-12938
1.5ENST000003400935ENSE00000710856chr19:44159725-44159591135UPAR_HUMAN158-203461U:140-18142
1.6ENST000003400936ENSE00000847435chr19:44156523-44156377147UPAR_HUMAN203-252501U:181-23050
1.7ENST000003400937ENSE00000847434chr19:44153295-44152732564UPAR_HUMAN252-335841U:230-275 (gaps)46

2.3cENST000003727643cENSE00001820360chr10:75670915-7567097662UROK_HUMAN-00--
2.4bENST000003727644bENSE00002193721chr10:75671283-7567137088UROK_HUMAN1-19190--
2.5ENST000003727645ENSE00001276413chr10:75671799-7567182628UROK_HUMAN20-29100--
2.6aENST000003727646aENSE00001169210chr10:75671973-75672080108UROK_HUMAN29-65371A:11-4535
2.7bENST000003727647bENSE00001169200chr10:75672682-75672856175UROK_HUMAN65-123591A:45-10359
2.8ENST000003727648ENSE00000834105chr10:75673048-7567313992UROK_HUMAN123-154321A:103-13230
2.9bENST000003727649bENSE00001169184chr10:75673297-75673516220UROK_HUMAN154-227740--
2.10ENST0000037276410ENSE00001169178chr10:75673738-75673886149UROK_HUMAN227-277510--
2.11ENST0000037276411ENSE00001169173chr10:75674534-75674674141UROK_HUMAN277-324480--
2.13ENST0000037276413ENSE00001169164chr10:75675009-75675157149UROK_HUMAN324-373500--
2.14dENST0000037276414dENSE00001892698chr10:75676147-756772551109UROK_HUMAN374-431580--

(-) Sequences/Alignments

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:122
 aligned with UROK_HUMAN | P00749 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:122
                                    40        50        60        70        80        90       100       110       120       130       140       150  
          UROK_HUMAN     31 CDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCA  152
               SCOP domains d2fd6a1 A:11-49 automated matches      d2fd6a2 A:50-132 automated matches                                                  SCOP domains
               CATH domains 2fd6A01 A:11-49 Laminin                2fd6A02 A:50-132 Plasminogen Kringle 4                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.......eeee....ee.....ee................................hhhhh.......hhhhhh................eeeeee..eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------L----------- SAPs(SNPs)
                PROSITE (2) --------------------EGF_1       ------KRINGLE_2  PDB: A:49-131 UniProt: 69-151                                           - PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------KRINGLE_1    ------------------- PROSITE (3)
           Transcript 2 (1) Exon 2.6a  PDB: A:11-45            ---------------------------------------------------------Exon 2.8  PDB: A:103-132       Transcript 2 (1)
           Transcript 2 (2) ----------------------------------Exon 2.7b  PDB: A:45-103 UniProt: 65-123                   ----------------------------- Transcript 2 (2)
                2fd6 A   11 CDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCA  132
                                    20        30        40        50        60        70        80        90       100       110       120       130  

Chain H from PDB  Type:PROTEIN  Length:212
 aligned with Q924Q0_MOUSE | Q924Q0 from UniProtKB/TrEMBL  Length:143

    Alignment length:212
                                                                                                                                                                                                                              133               
                                                                                                                                                            131                                                            132  | 137  138  143 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|        -         -         -         -         -         -   |  |136|    | 142| 
        Q924Q0_MOUSE      1 QVQLQQPGAELVKPGASVKMSCKASGYTFTSYWITWVKQRPGQGLEWIGDIYPGSGSTNYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCAPDSNHLYFDYWGQGTTLTVSSESQSFPNVFPLVS--------------------------------------------------------------C--ESPLS----DKNLVA-    -
               SCOP domains d2fd6h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                        d2fd6h2 H:114-208 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 2fd6H01 H:1-114 Immunoglobulins                                                                                        2fd6H02 H:115-208 Immunoglobulins                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhh.eeeeeee......eeeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeee..........eeeeee.....eeee.hhh....eee...eee..eeeeeeee............eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fd6 H    1 GVKLQQSGPEVVKPGASVKISCKASGYSFTNFYIHWVKQRPGQGLEWIGWIFHGSDNTEYNEKFKDKATLTADTSSSTAYMQLSSLTSEDSAVYFCARWGPHWYFDVWGQGTTVTVSSAKTTPPSVYPLAPNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIAAA  208
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125||     136       146       156       166       176       186       196       206  
                                                                              52A                            82A||               100A                       126|                                                                                
                                                                                                              82B|                                           128                                                                                
                                                                                                               82C                                                                                                                              

Chain L from PDB  Type:PROTEIN  Length:214
 aligned with Q52L64_MOUSE | Q52L64 from UniProtKB/TrEMBL  Length:240

    Alignment length:222
                                                                                                                                                                                                                                                     240  
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
        Q52L64_MOUSE     21 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSYNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDHFSGSGSGTDFTLTISSVKAEDLALYYCQQYYNYPLTFGAGTKLDLRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC--    -
               SCOP domains d2fd6l1 L:1-106A Immunoglob       ulin light chain kappa variable domain, VL-kappa                               d2fd6l2 L:107-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                - SCOP domains
               CATH domains 2fd6L01 L:1-107 Immunoglobu       lins                                                                            2fd6L02 L:108-210 Immunoglobulins                                                                      ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee..-------....eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee-..........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2fd6 L    1 DIVLTQSPDITAASLGQKVTITCSASS-------SVSYMHWYQQKSGTSPKPWIFEISKLASGVPARFSGSGSGTSYSLTISSMEAEDAAIYYCQQ-WNYPFTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEAKA  215
                                    10        20      |  -    |   34        44        54        64        74        84     | |93||     104  |    113       123       133       143       153       163       173       183       193       203       213  
                                                     27      29                                                           90 | 94|       106A                                                                                                             
                                                                                                                            91  96                                                                                                                        

Chain U from PDB  Type:PROTEIN  Length:249
 aligned with UPAR_HUMAN | Q03405 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:276
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
          UPAR_HUMAN     22 GLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPD  297
               SCOP domains -d2fd6u1 U:1-80 Urokinase plasmino   gen activator surface receptor uPAR                    d2fd6u3 U:92-188 Urokinase plasminogen           activator surface receptor uPAR                 d2fd6u2 U:189-275 Urokinase plasminogen activator surface re   ceptor uPAR              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....eeeee......eeeeeeeeee.---.eeeeeeeee......eeeeeee..eeeeeeeeee.........-----------..eeeeee...........eeee......eeeeeeee.----------...eeeeeee.....eeeeeee..eeeeeeee...........hhhhh.eeeeeeeeeee...........eeeeee....eeeeeeeee....eeeeeeeee.hhhh.---hhhhhh....eeeee......... 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 1 (1) Exon 1.2  PDB: U:1A-33 [INCOMPLETE]-----------------------------------------------Exon 1.4  PDB: U:92-129 UniProt: 104-158 [INCOMPLETE]  --------------------------------------------Exon 1.6  PDB: U:181-230 UniProt: 203-252         --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: U:37-80 UniProt: 56-104           -----------------------------------------------------Exon 1.5  PDB: U:140-181 UniProt: 158-203     ------------------------------------------------Exon 1.7  PDB: U:230-275 (gaps) [INCOMPLETE]   Transcript 1 (2)
                2fd6 U   1A SLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWE---ELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGN-----------YLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHW----------DDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQ---LGDAFSMNHIDVSCCTKSGCNHPD  275
                            |        9        19        29   |   |39        49        59        69        79|        -  |     99       109       119       129         -|      149       159       169       179       189       199       209       219       229       239        |-  |    259       269      
                           1A                               33  37                                         80          92                                  129        140                                                                                                         248 252                       

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (7, 9)

Asymmetric Unit

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FD6)

(-) Gene Ontology  (74, 84)

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 H   (Q924Q0_MOUSE | Q924Q0)

Chain L   (Q52L64_MOUSE | Q52L64)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UPAR_HUMAN | Q034051ywh 2i9b 3bt1 3bt2 3u73 3u74 4k24 4qti
        UROK_HUMAN | P007491c5w 1c5x 1c5y 1c5z 1ejn 1f5k 1f5l 1f92 1fv9 1gi7 1gi8 1gi9 1gj7 1gj8 1gj9 1gja 1gjb 1gjc 1gjd 1kdu 1lmw 1o3p 1o5a 1o5b 1o5c 1owd 1owe 1owh 1owi 1owj 1owk 1sc8 1sqa 1sqo 1sqt 1u6q 1urk 1vj9 1vja 1w0z 1w10 1w11 1w12 1w13 1w14 2i9a 2i9b 2nwn 2o8t 2o8u 2o8w 2r2w 2vin 2vio 2vip 2viq 2viv 2viw 2vnt 3bt1 3bt2 3ig6 3kgp 3khv 3kid 3m61 3mhw 3mwi 3ox7 3oy5 3oy6 3pb1 3qn7 3u73 4dva 4dw2 4fu7 4fu8 4fu9 4fub 4fuc 4fud 4fue 4fuf 4fug 4fuh 4fui 4fuj 4gly 4h42 4jk5 4jk6 4jni 4jnl 4k24 4mnv 4mnw 4mnx 4mny 4os1 4os2 4os4 4os5 4os6 4os7 4x0w 4x1n 4x1p 4x1q 4x1r 4x1s 4xsk 4zhl 4zhm 4zkn 4zko 4zkr 4zks 5hgg
UniProtKB/TrEMBL
        Q52L64_MOUSE | Q52L641a3r 1bbd 1h3p 1jgu 1jgv 1q9w 2r1w 2r1x 2r1y 2r23 2r2b 2r2h 3t77

(-) Related Entries Specified in the PDB File

2fat CRYSTAL STRUCTURE OF ATN-615