3BT2: Urokinase-type plasminogen activator
Structure of urokinase receptor, urokinase and vitronectin complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 25 Mar 2008.
- Method
- X-ray diffraction
- Resolution
- 2.5 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 5
- Atoms
- 6,654
- Mol. weight
- 98.92 kDa
- Ligands
- NAG
- Released
- 25 Mar 2008
Explore 3BT2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3BT2 contains 27 α-helices and 80 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 4 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 1 |
| α-helix | 23-25 | 3 | |
| β-strand | 28-32 | 5 | 1 |
| β-strand | 37-38 | 2 | 2 |
| β-strand | 44-45 | 2 | 2 |
| β-strand | 51 | 1 | 3 |
| β-strand | 64 | 1 | 4 |
| β-strand | 65 | 1 | 5 |
| β-strand | 70 | 1 | 4 |
| α-helix | 71-73 | 3 | |
| α-helix | 79-81 | 3 | |
| α-helix | 91-94 | 4 | |
| β-strand | 103 | 1 | 6 |
| β-strand | 112-117 | 6 | 6 |
| β-strand | 120-125 | 6 | 6 |
| β-strand | 126 | 1 | 5 |
| β-strand | 130 | 1 | 3 |
Chain B: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20 | 1 | 7 |
| β-strand | 31 | 1 | 7 |
| α-helix | 34-37 | 4 | |
Chain H: 8 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 13 |
| β-strand | 10-12 | 3 | 14 |
| β-strand | 18-25 | 8 | 13 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 14 |
| β-strand | 46-52 | 7 | 14 |
| β-strand | 53-59 | 7 | 14 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-72 | 6 | 13 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-82 | 6 | 13 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-95 | 8 | 14 |
| β-strand | 100A-103 | 4 | 14 |
| β-strand | 107-111 | 5 | 14 |
| β-strand | 117 | 1 | 15 |
| α-helix | 118-119 | 2 | |
| β-strand | 120-124 | 5 | 16 |
| β-strand | 132-140 | 9 | 16 |
| β-strand | 141 | 1 | 15 |
| β-strand | 146-149 | 4 | 17 |
| α-helix | 150-152 | 3 | |
| β-strand | 154 | 1 | 17 |
| β-strand | 158-160 | 3 | 16 |
| α-helix | 161-163 | 3 | |
| β-strand | 164-166 | 3 | 16 |
| β-strand | 169-177 | 9 | 16 |
| β-strand | 189-194 | 6 | 17 |
| α-helix | 195-197 | 3 | |
| β-strand | 199-204 | 6 | 17 |
Chain L: 8 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 8 |
| β-strand | 10-13 | 4 | 9 |
| β-strand | 19-25 | 7 | 8 |
| β-strand | 33-38 | 6 | 9 |
| β-strand | 45-49 | 5 | 9 |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 55 | 1 | |
| β-strand | 62-67 | 6 | 8 |
| β-strand | 70-75 | 6 | 8 |
| α-helix | 80-82 | 3 | |
| β-strand | 84-90 | 7 | 9 |
| α-helix | 97 | 1 | |
| β-strand | 98 | 1 | 9 |
| α-helix | 99 | 1 | |
| β-strand | 102-106 | 5 | 9 |
| β-strand | 110 | 1 | 10 |
| β-strand | 113-117 | 5 | 11 |
| α-helix | 118-120 | 3 | |
| α-helix | 121-125 | 5 | |
| β-strand | 128-138 | 11 | 11 |
| β-strand | 139 | 1 | 10 |
| β-strand | 144-149 | 6 | 12 |
| β-strand | 152-154 | 3 | 12 |
| β-strand | 158-162 | 5 | 11 |
| α-helix | 163-166 | 4 | |
| β-strand | 172-181 | 10 | 11 |
| α-helix | 182-186 | 5 | |
| β-strand | 190-196 | 7 | 12 |
| β-strand | 204-209 | 6 | 12 |
Chain U: 6 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 18 |
| β-strand | 12-16 | 5 | 18 |
| α-helix | 17-18 | 2 | |
| β-strand | 23-33 | 11 | 18 |
| β-strand | 36-46 | 11 | 18 |
| β-strand | 53-59 | 7 | 18 |
| β-strand | 62-71 | 10 | 18 |
| α-helix | 76-78 | 3 | |
| β-strand | 94-97 | 4 | 19 |
| β-strand | 98-99 | 2 | 18 |
| α-helix | 100-102 | 3 | |
| β-strand | 111-114 | 4 | 19 |
| β-strand | 121-129 | 9 | 18 |
| β-strand | 140 | 1 | 1 |
| β-strand | 143-149 | 7 | 18 |
| β-strand | 155-161 | 7 | 18 |
| β-strand | 164-171 | 8 | 18 |
| α-helix | 181-182 | 2 | |
| α-helix | 184-186 | 3 | |
| β-strand | 189-196 | 8 | 20 |
| β-strand | 197-199 | 3 | 18 |
| β-strand | 200 | 1 | 21 |
| β-strand | 204 | 1 | 21 |
| β-strand | 211-216 | 6 | 20 |
| β-strand | 221-229 | 9 | 18 |
| β-strand | 234-242 | 9 | 18 |
| α-helix | 244-247 | 4 | |
| β-strand | 262-266 | 5 | 18 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Urokinase-type plasminogen activator | A | protein | 135 | Homo sapiens | P00749 (AlphaFold model) |
| Vitronectin | B | protein | 40 | Homo sapiens | P04004 (AlphaFold model) |
| anti-uPAR antibody, light chain | L | protein | 212 | Mus musculus | P01675 (AlphaFold model), P01837 (AlphaFold model) |
| anti-uPAR antibody, heavy chain | H | protein | 214 | Mus musculus | |
| Urokinase plasminogen activator surface receptor | U | protein | 283 | Homo sapiens | Q03405 |
Sequence of entity 1 (A), FASTA
>3BT2_1 Urokinase-type plasminogen activator (chains A)
RSSNELHQVPSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFY
RGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVG
LKPLVQECMVHDCAD
Sequence of entity 2 (B), FASTA
>3BT2_2 Vitronectin (chains B)
QESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKP
Sequence of entity 3 (L), FASTA
>3BT2_3 anti-uPAR antibody, light chain (chains L)
DIVLTQSPDITAASLGQKVTITCSASSSVSYMHWYQQKSGTSPKPWIFEISKLASGVPAR
FSGSGSGTSYSLTISSMEAEDAAIYYCQQWNYPFTFGGGTKLEIKRADAAPTVSIFPPSS
EQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLT
KDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
Sequence of entity 4 (H), FASTA
>3BT2_4 anti-uPAR antibody, heavy chain (chains H)
GVKLQQSGPEVVKPGASVKISCKASGYSFTNFYIHWVKQRPGQGLEWIGWIFHGSDNTEY
NEKFKDKATLTADTSSSTAYMQLSSLTSEDSAVYFCARWGPHWYFDVWGQGTTVTVSSAK
TTPPSVYPLAPGNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVPSSTWPSETVTCNVAHPASSTKVDKKIAAAG
Sequence of entity 5 (U), FASTA
>3BT2_5 Urokinase plasminogen activator surface receptor (chains U)
RSLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYR
TGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSP
EEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNE
GPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMV
RGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Primary citation
Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes. Huai, Q., Zhou, A., Lin, L. et al. Nat Struct Mol Biol (2008) 15:422-423. DOI 10.1038/nsmb.1404 · PubMed
Other PDB entries of the same protein (UniProt P00749 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5YC6 1.18 Å, The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH4.6
- 4ZKO 1.29 Å, The crystal structure of upain-1-W3A in complex with uPA at pH7.4
- 4ZKN 1.36 Å, The crystal structure of upain-1-W3A in complex with uPA at pH5.5
- 4ZKR 1.36 Å, The crystal structure of upain-1-W3A in complex with uPA at pH9.0
- 6XVD 1.4 Å, Crystal structure of complex of urokinase and a upain-1 variant(W3F) in pH7.4 condition
- 2O8T 1.45 Å, Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator…
- 3MHW 1.45 Å, The complex crystal Structure of Urokianse and 2-Aminobenzothiazole
- 5Z1C 1.45 Å, The crystal structure of uPA in complex with 4-Iodobenzylamine at pH7.4
- 5WXF 1.46 Å, Crystal structure of uPA in complex with upain-2-2
- 4MNW 1.49 Å, Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic…
- 1GJ7 1.5 Å, Engineering inhibitors highly selective for the S1 sites of SER190 trypsin-like serine…
- 4XSK 1.5 Å, Structure of PAItrap, an uPA mutant
Browse structure collections
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