T0461

X-ray Targets
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T0461

tRNA-specific adenosine-34 deaminase subunit ADAT2 from Homo sapiens

Target type: Server only

Target sequence:

>T0461 DEAD1CA, Homo sapiens, 189 residues
MHHHHHHSSGVDLGTENLYFQSMEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYKQENPNAPKSKVRK

Structure:
Method: X-ray, res=2.8Å, R/Rfree=0.21/0.26
Determined by: SGC
PDB ID: 3dh1

3dh1_A cartoon
Cartoon diagram of 461: 3dh1 chain A

PyMOL of 3dh1

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Cytidine deaminase fold, which is a circular permutation of thioredoxin fold.

CASP category:

Comparative modeling:easy.

Closest templates:

2nx8, 2b3j, 1z3a, 1wwr, 2a8n.

Target sequence - PDB file inconsistencies:

T0461    3dh1.pdb    T0461.pdb    PyMOL    PyMOL of domains    

T0461    1 MHHHHHHSSGVDLGTENLYFQSMEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYKQENPNAPKSKVRK 189
           ~~~~~~~~~~~~~~~||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~~~~~~~
3dh1A   12 ---------------ENLYFQSMEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYKQ------------ 173

Single domain protein: target 16-177 ; pdb 12-173

Sequence classification:

Cytidine and deoxycytidylate deaminase family (dCMP_cyt_deam_1) in Pfam.

Server predictions:

T0461:pdb 12-173:seq 16-177:CM_easy;   alignment

distribution of first scores
First models for T0461: Gaussian kernel density estimation for GDT-TS scores of the first server models, plotted at various bandwidths (=standard deviations). The GDT-TS scores are shown as a spectrum along the horizontal axis: each bar represents first server model. The bars are colored green, gray and black for top 10, bottom 25% and the rest of servers. The family of curves with varying bandwidth is shown. Bandwidth varies from 0.3 to 8.2 GDT-TS % units with a step of 0.1, which corresponds to the color ramp from magenta through blue to cyan. Thicker curves: red, yellow-framed brown and black, correspond to bandwidths 1, 2 and 4 respectively.

click on a score in the table below to display the model in PyMOL

# GROUP ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ ↓ GROUP #
T0461 T0461 T0461 T0461
First score First Z-score Best score Best Z-score
1 SAM−T08−server 85.49 80.04 90.34 1.05 1.16 1.01 85.49 80.04 90.34 1.14 1.11 1.08 SAM−T08−server 1
2 LEE−SERVER 84.57 79.01 88.89 0.91 1.03 0.84 84.57 79.01 88.89 0.95 0.93 0.85 LEE−SERVER 2
3 Zhang−Server 83.64 79.94 88.33 0.77 1.15 0.77 84.11 80.56 88.64 0.85 1.21 0.81 Zhang−Server 3
4 MUProt 83.33 75.00 87.90 0.72 0.51 0.72 83.33 79.27 88.01 0.69 0.97 0.71 MUProt 4
5 Phyre_de_novo 83.33 67.69 87.89 0.72 -0.43 0.72 83.33 79.11 87.89 0.69 0.95 0.69 Phyre_de_novo 5
6 MULTICOM−REFINE 82.87 79.27 88.01 0.65 1.06 0.73 83.33 79.27 88.01 0.69 0.97 0.71 MULTICOM−REFINE 6
7 MULTICOM−CLUSTER 82.87 77.83 86.33 0.65 0.88 0.54 83.18 77.83 86.33 0.66 0.71 0.45 MULTICOM−CLUSTER 7
8 MULTICOM−RANK 82.87 73.51 88.23 0.65 0.32 0.76 82.87 76.75 88.23 0.59 0.52 0.75 MULTICOM−RANK 8
9 HHpred5 82.72 80.25 86.53 0.63 1.19 0.56 82.72 80.25 86.53 0.56 1.15 0.48 HHpred5 9
10 GS−MetaServer2 82.72 77.06 84.88 0.63 0.78 0.36 82.72 77.06 84.88 0.56 0.57 0.22 GS−MetaServer2 10
11 RAPTOR 82.72 75.10 87.21 0.63 0.52 0.64 82.72 76.18 87.21 0.56 0.42 0.59 RAPTOR 11
12 Fiser−M4T 82.72 74.18 85.47 0.63 0.41 0.43 82.72 74.18 85.47 0.56 0.05 0.32 Fiser−M4T 12
13 MUSTER 82.56 75.46 86.29 0.60 0.57 0.53 82.56 76.13 86.29 0.53 0.41 0.44 MUSTER 13
14 Frankenstein 82.56 74.13 85.97 0.60 0.40 0.49 82.56 74.13 85.97 0.53 0.04 0.39 Frankenstein 14
15 PS2−server 82.41 74.69 86.38 0.58 0.47 0.54 82.41 74.69 86.38 0.50 0.15 0.46 PS2−server 15
16 HHpred2 82.41 72.99 86.58 0.58 0.25 0.56 82.41 72.99 86.58 0.50 -0.16 0.49 HHpred2 16
17 BAKER−ROBETTA 82.25 76.90 88.48 0.56 0.76 0.79 83.95 76.90 88.48 0.82 0.55 0.79 BAKER−ROBETTA 17
18 Poing 82.10 77.26 87.61 0.53 0.80 0.69 82.10 78.14 87.61 0.43 0.77 0.65 Poing 18
19 Phyre2 82.10 77.26 87.66 0.53 0.80 0.69 82.10 78.60 87.66 0.43 0.85 0.66 Phyre2 19
20 Phragment 82.10 77.26 87.66 0.53 0.80 0.69 82.10 78.34 87.66 0.43 0.81 0.66 Phragment 20
21 forecast 82.10 75.51 85.94 0.53 0.58 0.49 82.10 76.80 86.19 0.43 0.53 0.43 forecast 21
22 COMA−M 82.10 73.77 85.56 0.53 0.35 0.44 84.88 76.80 87.24 1.02 0.53 0.59 COMA−M 22
23 fais−server 81.79 74.79 86.40 0.49 0.48 0.54 82.10 78.09 86.40 0.43 0.76 0.46 fais−server 23
24 METATASSER 81.48 69.91 87.78 0.44 -0.15 0.71 82.72 76.13 87.78 0.56 0.41 0.68 METATASSER 24
25 HHpred4 81.17 77.47 85.41 0.39 0.83 0.43 81.17 77.47 85.41 0.24 0.65 0.31 HHpred4 25
26 pro−sp3−TASSER 80.86 63.73 84.84 0.35 -0.94 0.36 82.25 76.70 88.37 0.46 0.51 0.77 pro−sp3−TASSER 26
27 Pcons_dot_net 80.56 75.62 83.49 0.30 0.59 0.20 83.49 77.88 87.41 0.72 0.72 0.62 Pcons_dot_net 27
28 Pcons_multi 80.56 75.62 83.49 0.30 0.59 0.20 82.87 78.45 87.42 0.59 0.83 0.62 Pcons_multi 28
29 BioSerf 80.56 72.43 86.27 0.30 0.18 0.53 80.56 72.43 86.27 0.11 -0.26 0.44 BioSerf 29
30 SAM−T02−server 80.40 71.97 84.15 0.28 0.12 0.28 80.40 74.74 84.15 0.07 0.15 0.11 SAM−T02−server 30
31 nFOLD3 80.25 72.02 83.96 0.25 0.13 0.26 80.25 72.17 83.96 0.04 -0.31 0.08 nFOLD3 31
32 MULTICOM−CMFR 80.25 71.81 85.58 0.25 0.10 0.45 82.41 75.10 85.90 0.50 0.22 0.38 MULTICOM−CMFR 32
33 Pcons_local 80.09 71.45 83.77 0.23 0.05 0.23 80.56 76.29 83.77 0.11 0.44 0.05 Pcons_local 33
34 FFASstandard 79.94 76.03 81.21 0.21 0.64 -0.07 80.86 76.18 85.84 0.17 0.42 0.37 FFASstandard 34
35 FFASsuboptimal 79.94 76.03 81.21 0.21 0.64 -0.07 79.94 76.03 81.21 -0.02 0.39 -0.35 FFASsuboptimal 35
36 GS−KudlatyPred 79.94 74.59 84.52 0.21 0.46 0.32 79.94 74.79 84.52 -0.02 0.16 0.17 GS−KudlatyPred 36
37 COMA 79.78 75.26 83.78 0.18 0.54 0.23 82.87 75.26 87.24 0.59 0.25 0.59 COMA 37
38 keasar−server 79.78 75.05 84.34 0.18 0.52 0.30 81.94 77.16 85.70 0.40 0.59 0.35 keasar−server 38
39 3D−JIGSAW_AEP 79.78 67.85 81.32 0.18 -0.41 -0.06 80.09 69.70 81.72 0.01 -0.76 -0.27 3D−JIGSAW_AEP 39
40 PSI 79.78 64.15 84.40 0.18 -0.89 0.31 79.78 72.38 84.40 -0.06 -0.27 0.15 PSI 40
41 FAMSD 79.63 76.03 84.96 0.16 0.64 0.37 81.79 76.03 84.99 0.37 0.39 0.24 FAMSD 41
42 3DShot2 79.32 68.72 84.16 0.11 -0.30 0.28 79.32 68.72 84.16 -0.15 -0.94 0.11 3DShot2 42
43 3D−JIGSAW_V3 79.17 76.49 82.30 0.09 0.70 0.06 79.17 76.49 82.39 -0.18 0.47 -0.16 3D−JIGSAW_V3 43
44 GeneSilicoMetaServer 79.01 74.59 82.41 0.07 0.46 0.07 81.17 74.59 84.16 0.24 0.13 0.11 GeneSilicoMetaServer 44
45 SAM−T06−server 78.86 60.55 83.57 0.04 -1.35 0.21 80.40 71.97 84.01 0.07 -0.35 0.09 SAM−T06−server 45
46 circle 78.70 69.55 82.65 0.02 -0.19 0.10 79.94 75.31 83.19 -0.02 0.26 -0.04 circle 46
47 FALCON_CONSENSUS 77.93 72.58 83.17 -0.10 0.20 0.16 77.93 72.69 83.19 -0.44 -0.22 -0.04 FALCON_CONSENSUS 47
48 FALCON 77.78 72.02 82.50 -0.12 0.13 0.08 77.93 72.69 83.19 -0.44 -0.22 -0.04 FALCON 48
49 huber−torda−server 77.31 60.65 79.67 -0.19 -1.34 -0.25 77.31 60.65 79.67 -0.58 -2.40 -0.59 huber−torda−server 49
50 FFASflextemplate 77.16 72.94 79.11 -0.21 0.25 -0.32 78.70 75.21 80.40 -0.28 0.24 -0.47 FFASflextemplate 50
51 CpHModels 77.01 71.55 78.52 -0.24 0.07 -0.39 77.01 71.55 78.52 -0.64 -0.42 -0.77 CpHModels 51
52 mGenTHREADER 76.70 67.03 80.52 -0.28 -0.52 -0.15 76.70 67.03 80.52 -0.70 -1.24 -0.45 mGenTHREADER 52
53 Pushchino 76.39 64.97 79.13 -0.33 -0.78 -0.31 76.39 64.97 79.13 -0.77 -1.61 -0.67 Pushchino 53
54 Distill 75.62 70.37 73.20 -0.45 -0.09 -1.01 75.62 70.94 73.23 -0.93 -0.53 -1.59 Distill 54
55 3Dpro 73.61 67.75 76.06 -0.75 -0.42 -0.68 73.61 69.19 76.06 -1.35 -0.85 -1.15 3Dpro 55
56 FEIG 70.83 60.65 72.72 -1.17 -1.34 -1.07 81.02 73.10 85.43 0.21 -0.14 0.31 FEIG 56
57 LOOPP_Server 69.60 54.42 67.78 -1.36 -2.14 -1.65 82.87 74.02 86.91 0.59 0.02 0.54 LOOPP_Server 57
58 panther_server 68.67 63.32 64.24 -1.50 -1.00 -2.07 79.94 76.65 80.40 -0.02 0.50 -0.47 panther_server 58
59 MUFOLD−Server 68.67 59.26 70.18 -1.50 -1.52 -1.37 68.67 63.68 70.18 -2.39 -1.85 -2.07 MUFOLD−Server 59
60 FUGUE_KM 64.51 60.91 61.04 -2.13 -1.31 -2.45 64.51 60.91 61.04 -3.27 -2.35 -3.49 FUGUE_KM 60
61 ACOMPMOD 59.72 55.71 57.32 -2.86 -1.98 -2.89 67.44 61.57 66.86 -2.65 -2.23 -2.58 ACOMPMOD 61
62 rehtnap 42.75 30.71 34.02 -5.43 -5.20 -5.64 45.06 35.03 35.81 -7.36 -7.04 -7.42 rehtnap 62
63 FOLDpro 36.42 33.44 29.99 -6.39 -4.85 -6.11 58.33 49.74 52.08 -4.57 -4.37 -4.89 FOLDpro 63
64 MUFOLD−MD 29.32 23.10 40.47 -7.46 -6.18 -4.88 32.25 28.65 40.47 -10.05 -8.19 -6.69 MUFOLD−MD 64
65 RBO−Proteus 24.38 22.02 35.82 -8.21 -6.32 -5.42 24.38 22.12 36.72 -11.70 -9.37 -7.28 RBO−Proteus 65
66 mariner1 22.22 18.98 31.10 -8.54 -6.71 -5.98 56.17 47.53 54.35 -5.02 -4.77 -4.53 mariner1 66
67 RANDOM 16.20 13.08 16.20 -9.45 -7.48 -7.74 16.20 13.08 16.20 -13.42 -11.01 -10.48 RANDOM 67
68 mahmood−torda−server 14.51 12.45 18.56 -9.71 -7.56 -7.46 14.51 12.45 18.56 -13.78 -11.12 -10.11 mahmood−torda−server 68
69 schenk−torda−server 13.58 11.63 16.42 -9.85 -7.66 -7.71 16.51 13.63 16.85 -13.36 -10.91 -10.37 schenk−torda−server 69
70 OLGAFS 11.11 9.88 12.49 -10.22 -7.89 -8.18 14.35 12.91 12.54 -13.81 -11.04 -11.05 OLGAFS 70
71 BHAGEERATH                   -9.45 -7.48 -7.74                   -13.42 -11.01 -10.48 BHAGEERATH 71
72 YASARA                   -9.45 -7.48 -7.74                   -13.42 -11.01 -10.48 YASARA 72
73 pipe_int                   -9.45 -7.48 -7.74                   -13.42 -11.01 -10.48 pipe_int 73
74 test_http_server_01                   -9.45 -7.48 -7.74                   -13.42 -11.01 -10.48 test_http_server_01 74