Programmed cell death protein 1

UniProt data

UniProt name: PDCD1_HUMAN (Q15116)

Gene name: PDCD1; Synonyms=PD1

Organism: Homo sapiens (Human).

Function: Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen- specific manner. Possible cell death inducer, in association with other factors. {ECO:0000269|PubMed:21276005}.

Subcellular location: Membrane; Single-pass type I membrane protein.

Transmembrane domains:

  1. 171-191, 21 AA, Helical. {ECO:0000255}.

Sequence: 288 AA

10 20 30 40 50 60 MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA TFTCSFSNTS 70 80 90 100 110 120 ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL PNGRDFHMSV VRARRNDSGT 130 140 150 160 170 180 YLCGAISLAP KAQIKESLRA ELRVTERRAE VPTAHPSPSP RPAGQFQTLV VGVVGGLLGS 190 200 210 220 230 240 LVLLVWVLAV ICSRAARGTI GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP 250 260 270 280 CVPEQTEYAT IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL

CATM prediction

The sequence of PDCD1_HUMAN returned 6 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
    170       180       190  
  |    +    |    +    |    		 (Å) (°) (Å) (°)  
Model 1 TLVVGVVGGLLGSLVLLVWVLAVICSR 6.4 -46.8° 4.8 55.7 -29.9
Model 2 TLVVGVVGGLLGSLVLLVWVLAVICSR 7.3 -26.0° 1.9 49.0 -21.2
Model 3 TLVVGVVGGLLGSLVLLVWVLAVICSR 6.3 -54.1° 4.8 41.0 -21.1
Model 4 TLVVGVVGGLLGSLVLLVWVLAVICSR 7.2 -53.9° 3.6 35.6 -16.4
Model 5 TLVVGVVGGLLGSLVLLVWVLAVICSR 6.7 +53.0° 2.7 87.7 -10.7
Model 6 TLVVGVVGGLLGSLVLLVWVLAVICSR 7.4 -50.0° 2.9 47.0 -2.2

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, 173, VAL, HA A, 172, GLY, O 2.45Å
B, 176, GLY, HA1 A, 173, VAL, O 3.06Å
A, 173, VAL, HA B, 172, GLY, O 2.45Å
A, 176, GLY, HA1 B, 173, VAL, O 3.06Å