Syndecan-1

UniProt data

UniProt name: SDC1_HUMAN (P18827)

Gene name: SDC1; Synonyms=SDC

Organism: Homo sapiens (Human).

Function: Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413). {ECO:0000269|PubMed:22660413}.

Subcellular location: Membrane {ECO:0000255}; Single-pass type I membrane protein {ECO:0000255}. Secreted {ECO:0000269|PubMed:9169435}. Secreted, exosome {ECO:0000269|PubMed:22660413}. Note=Shedding of the ectodomain produces a soluble form. {ECO:0000269|PubMed:9169435}.

Transmembrane domains:

  1. 255-275, 21 AA, Helical. {ECO:0000255}.

Sequence: 310 AA

10 20 30 40 50 60 MRRAALWLWL CALALSLQPA LPQIVATNLP PEDQDGSGDD SDNFSGSGAG ALQDITLSQQ 70 80 90 100 110 120 TPSTWKDTQL LTAIPTSPEP TGLEATAAST STLPAGEGPK EGEAVVLPEV EPGLTAREQE 130 140 150 160 170 180 ATPRPRETTQ LPTTHLASTT TATTAQEPAT SHPHRDMQPG HHETSTPAGP SQADLHTPHT 190 200 210 220 230 240 EDGGPSATER AAEDGASSQL PAAEGSGEQD FTFETSGENT AVVAVEPDRR NQSPVDQGAT 250 260 270 280 290 300 GASQGLLDRK EVLGGVIAGG LVGLIFAVCL VGFMLYRMKK KDEGSYSLEE PKQANGGAYQ KPTKQEEFYA

CATM prediction

The sequence of SDC1_HUMAN returned 7 potential models

The positions at the dimer's interface are highlighted in yellow. The position at the crossing point is highlighted in orange.

# Sequence and interface d θ Z' ω' Score
          260       270      
   +    |    +    |    +   		 (Å) (°) (Å) (°)  
Model 1 VLGGVIAGGLVGLIFAVCLVGFMLYRM 6.5 -33.9° 1.7 56.9 -42.3
Model 2 VLGGVIAGGLVGLIFAVCLVGFMLYRM 6.5 -42.9° 3.9 53.8 -31.4
Model 3 VLGGVIAGGLVGLIFAVCLVGFMLYRM 6.3 -51.2° 6.0 45.0 -28.2
Model 4 VLGGVIAGGLVGLIFAVCLVGFMLYRM 7.0 -43.0° 4.5 35.2 -26.8
Model 5 VLGGVIAGGLVGLIFAVCLVGFMLYRM 6.5 -54.8° 0.3 45.3 -26.3
Model 6 VLGGVIAGGLVGLIFAVCLVGFMLYRM 6.5 -52.9° 5.2 58.2 -21.3
Model 7 VLGGVIAGGLVGLIFAVCLVGFMLYRM 7.1 -40.0° 2.7 34.0 -11.8

Click on the model number to visualize its details below.

MODEL 1 DETAILS

Precited structure:


Click on the image to enlarge

Download model 1 structure: PDB, PyMOL session

List of hydrogen bonds:

Donor Acceptor Distance
B, 256, VAL, HA A, 255, GLY, O 2.53Å
B, 259, GLY, HA1 A, 256, VAL, O 2.75Å
B, 260, GLY, HA2 A, 259, GLY, O 2.82Å
A, 256, VAL, HA B, 255, GLY, O 2.53Å
A, 259, GLY, HA1 B, 256, VAL, O 2.75Å
A, 260, GLY, HA2 B, 259, GLY, O 2.82Å