T0394

X-ray Targets
387 388 389 390
391 392 393 394
395 396 397 398
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407 408 409 410
411 412 413 414
415 416 417 418
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483 485 486 487
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T0394

TP53-induced glycolysis and apoptosis regulator protein from Homo sapiens

Target type: Server only

Target sequence:

>T0394 chr_12_orf_5 , homo sapiens, 275 residues
NLYFQSARFALTVVRHGETRFNKEKIIQGQGVDEPLSETGFKQAAAAGIFLNNVKFTHAFSSDLMRTKQTMHGILERSKFCKDMTVKYDSRLRERKYGVVEGKALSELRAMAKAAREECPVFTPPGGETLDQVKMRGIDFFEFLCQLILKEADQKEQFSQGSPSNCLETSLAEIFPLGKNHSSKVNSDSGIPGLAASVLVVSHGAYMRSLFDYFLTDLKCSLPATLSRSELMSVTPNTGMSLFIINFEEGREVKPTVQCICMNLQDHLNGLTETR

Structure:
Method: X-ray, res=1.75Å, R/Rfree=0.18/0.23
Determined by: CESG
PDB ID: 3dcy

3dcy cartoon
Cartoon diagram of 394: 3dcy

PyMOL of 3dcy

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Phosphoglycerate mutase-like fold, which is a heavily elaborated thioredoxin-like structure.

CASP category:

Comparative modeling:hard, as elaborations of the core are quite different from the template.

Closest templates:

1xq9

Target sequence - PDB file inconsistencies:

Two internal loops and C-terminus are disordered. MSE is instead of MET.

T0394    3dcy.pdb    T0394.pdb    PyMOL    PyMOL of domains    

T0394    1 NLYFQSARFALTVVRHGETRFNKEKIIQGQGVDEPLSETGFKQAAAAGIFLNNVKFTHAFSSDLMRTKQTMHGILERSKFCKDMTVKYDSRLRERKYGVVEGKALSELRAMAKAAREECPVFTPPGGETLDQVKMRGIDFFEFLCQLILKEADQKEQFSQGSPSNCLETSLAEIFPLGKNHSSKVNSDSGIPGLAASVLVVSHGAYMRSLFDYFLTDLKCSLPATLSRSELMSVTPNTGMSLFIINFEEGREVKPTVQCICMNLQDHLNGLTETR 275
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~~~~|||||||||||||~~~~~~~~~~~~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~
3dcyA   -4 NLYFQSARFALTVVRHGETRFNKEKIIQGQGVDEPLSETGFKQAAAAGIFLNNVKFTHAFSSDLMRTKQTMHGILERSKFCKDMTVKYDSRLRERKYGVVEGKALSELRAMAKAAREECPVFTPPGGETLDQVKMRGIDFFEFLCQLILKEADQK---------NCLETSLAEIFPL-------------IPGLAASVLVVSHGAYMRSLFDYFLTDLKCSLPATLSRSELMSVTPNTGMSLFIINFEEGREVKPTVQCICMNLQDHLN------ 264

Residue change log: change 60, 66, 79, 106, 130, 202, 227, 235, 257, MSE to MET;

Single domain protein: target 1-155, 165-177, 191-269 ; pdb -4-150, 160-172, 186-264

Sequence classification:

Phosphoglycerate mutase family PGAM in Pfam.

Comments:

This protein is a close homolog of T0428.

Server predictions:

T0394:pdb -4-264:seq 1-269:CM_hard;   alignment

distribution of first scores
First models for T0394: 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 #
T0394 T0394 T0394 T0394
First score First Z-score Best score Best Z-score
1 Phyre_de_novo 65.89 53.74 64.26 2.13 1.34 1.50 65.89 58.23 64.26 1.87 1.66 1.50 Phyre_de_novo 1
2 COMA 65.39 62.48 62.99 2.05 2.73 1.34 65.39 62.48 62.99 1.79 2.33 1.32 COMA 2
3 Phragment 65.39 58.30 61.66 2.05 2.07 1.18 65.39 58.30 61.66 1.79 1.67 1.13 Phragment 3
4 Poing 65.28 58.47 61.58 2.03 2.09 1.17 65.28 58.47 61.58 1.78 1.70 1.12 Poing 4
5 Phyre2 65.28 58.47 61.58 2.03 2.09 1.17 65.28 58.47 61.58 1.78 1.70 1.12 Phyre2 5
6 FAMSD 63.87 53.88 58.11 1.82 1.36 0.75 63.87 53.88 58.11 1.56 0.97 0.62 FAMSD 6
7 HHpred4 63.26 59.14 63.11 1.73 2.20 1.36 63.26 59.14 63.11 1.46 1.80 1.33 HHpred4 7
8 HHpred5 63.26 59.14 63.11 1.73 2.20 1.36 63.26 59.14 63.11 1.46 1.80 1.33 HHpred5 8
9 SAM−T08−server 63.26 57.05 60.73 1.73 1.87 1.07 63.26 58.94 60.73 1.46 1.77 0.99 SAM−T08−server 9
10 HHpred2 63.06 58.81 62.95 1.70 2.15 1.34 63.06 58.81 62.95 1.43 1.75 1.31 HHpred2 10
11 METATASSER 61.23 53.00 61.79 1.42 1.22 1.20 61.23 53.61 61.79 1.14 0.93 1.15 METATASSER 11
12 pro−sp3−TASSER 60.02 50.91 60.49 1.24 0.89 1.04 60.02 51.69 60.57 0.95 0.62 0.97 pro−sp3−TASSER 12
13 pipe_int 57.59 47.71 59.04 0.87 0.38 0.86 57.59 49.70 61.28 0.57 0.31 1.07 pipe_int 13
14 FEIG 56.98 50.57 56.15 0.78 0.84 0.51 56.98 50.57 56.15 0.48 0.45 0.34 FEIG 14
15 3DShot2 56.58 44.97 51.41 0.72 -0.05 -0.06 56.58 44.97 51.41 0.42 -0.44 -0.34 3DShot2 15
16 COMA−M 56.17 50.10 55.23 0.66 0.76 0.40 56.98 50.10 56.28 0.48 0.37 0.36 COMA−M 16
17 BioSerf 54.45 46.49 56.92 0.40 0.19 0.61 54.45 46.49 56.92 0.08 -0.20 0.45 BioSerf 17
18 SAM−T06−server 53.14 42.61 54.56 0.20 -0.43 0.32 60.02 58.13 54.56 0.95 1.64 0.11 SAM−T06−server 18
19 panther_server 52.13 43.49 50.15 0.05 -0.29 -0.21 56.78 51.05 51.33 0.45 0.52 -0.35 panther_server 19
20 MUProt 51.62 43.39 55.77 -0.03 -0.30 0.47 52.33 44.06 55.86 -0.25 -0.59 0.30 MUProt 20
21 nFOLD3 51.42 47.17 53.10 -0.06 0.30 0.14 51.42 47.17 53.95 -0.39 -0.09 0.02 nFOLD3 21
22 MULTICOM−RANK 51.42 45.55 54.80 -0.06 0.04 0.35 55.77 45.55 57.30 0.29 -0.35 0.50 MULTICOM−RANK 22
23 MULTICOM−CLUSTER 51.42 45.55 54.80 -0.06 0.04 0.35 51.92 45.55 56.43 -0.31 -0.35 0.38 MULTICOM−CLUSTER 23
24 Zhang−Server 51.22 44.06 58.21 -0.09 -0.20 0.76 51.82 44.60 59.74 -0.33 -0.50 0.85 Zhang−Server 24
25 MULTICOM−REFINE 51.22 43.59 55.78 -0.09 -0.27 0.47 51.52 43.83 55.78 -0.38 -0.62 0.29 MULTICOM−REFINE 25
26 circle 50.81 45.55 52.22 -0.15 0.04 0.04 63.36 58.97 57.56 1.48 1.78 0.54 circle 26
27 MUSTER 50.81 45.01 55.31 -0.15 -0.05 0.41 51.42 45.01 55.31 -0.39 -0.44 0.22 MUSTER 27
28 Pcons_local 50.71 45.92 54.09 -0.17 0.10 0.26 50.71 45.92 54.09 -0.50 -0.29 0.04 Pcons_local 28
29 Pcons_dot_net 50.71 45.92 54.09 -0.17 0.10 0.26 50.71 45.92 54.09 -0.50 -0.29 0.04 Pcons_dot_net 29
30 mariner1 50.71 44.43 47.08 -0.17 -0.14 -0.59 60.93 53.98 56.78 1.10 0.99 0.43 mariner1 30
31 LEE−SERVER 50.61 43.25 53.40 -0.18 -0.33 0.18 50.61 43.25 53.62 -0.52 -0.71 -0.02 LEE−SERVER 31
32 LOOPP_Server 50.61 43.02 51.75 -0.18 -0.36 -0.02 56.68 50.57 54.21 0.43 0.45 0.06 LOOPP_Server 32
33 Frankenstein 50.51 43.86 53.54 -0.20 -0.23 0.20 51.32 45.45 53.98 -0.41 -0.37 0.03 Frankenstein 33
34 Pcons_multi 50.51 43.08 54.47 -0.20 -0.35 0.31 50.51 43.35 55.29 -0.53 -0.70 0.22 Pcons_multi 34
35 RAPTOR 50.41 43.79 53.31 -0.22 -0.24 0.17 50.71 44.57 54.55 -0.50 -0.51 0.11 RAPTOR 35
36 PS2−server 49.70 43.02 53.02 -0.32 -0.36 0.13 50.41 43.56 54.55 -0.55 -0.67 0.11 PS2−server 36
37 GS−KudlatyPred 49.70 42.10 49.97 -0.32 -0.51 -0.24 49.70 42.10 49.97 -0.66 -0.90 -0.54 GS−KudlatyPred 37
38 GS−MetaServer2 49.59 45.34 51.05 -0.34 0.01 -0.10 50.30 45.34 51.83 -0.57 -0.38 -0.28 GS−MetaServer2 38
39 keasar−server 49.09 44.64 52.00 -0.41 -0.10 0.01 53.34 47.81 53.56 -0.09 0.01 -0.03 keasar−server 39
40 fais−server 48.89 43.62 54.14 -0.44 -0.27 0.27 55.77 53.20 54.14 0.29 0.86 0.05 fais−server 40
41 forecast 48.78 41.43 51.41 -0.46 -0.61 -0.06 61.13 55.47 55.78 1.13 1.22 0.29 forecast 41
42 3D−JIGSAW_V3 48.58 42.44 52.24 -0.49 -0.45 0.04 48.58 42.44 52.32 -0.83 -0.84 -0.21 3D−JIGSAW_V3 42
43 MULTICOM−CMFR 48.28 41.19 53.29 -0.54 -0.65 0.17 49.70 43.45 54.24 -0.66 -0.68 0.07 MULTICOM−CMFR 43
44 GeneSilicoMetaServer 48.18 41.43 50.28 -0.55 -0.61 -0.20 48.38 43.99 50.53 -0.87 -0.60 -0.46 GeneSilicoMetaServer 44
45 mGenTHREADER 47.87 43.22 62.33 -0.60 -0.33 1.26 47.87 43.22 62.33 -0.95 -0.72 1.22 mGenTHREADER 45
46 FALCON_CONSENSUS 47.57 42.51 46.75 -0.64 -0.44 -0.63 50.81 44.43 52.50 -0.49 -0.53 -0.18 FALCON_CONSENSUS 46
47 FALCON 47.57 42.51 46.75 -0.64 -0.44 -0.63 50.81 44.43 52.50 -0.49 -0.53 -0.18 FALCON 47
48 PSI 47.57 42.51 46.75 -0.64 -0.44 -0.63 61.34 54.45 52.50 1.16 1.06 -0.18 PSI 48
49 ACOMPMOD 47.06 43.45 48.88 -0.72 -0.29 -0.37 47.06 43.45 48.88 -1.07 -0.68 -0.70 ACOMPMOD 49
50 Fiser−M4T 47.06 42.75 48.14 -0.72 -0.41 -0.46 47.06 42.75 48.14 -1.07 -0.79 -0.81 Fiser−M4T 50
51 3Dpro 46.96 42.31 50.39 -0.74 -0.48 -0.18 46.96 42.31 50.39 -1.09 -0.86 -0.48 3Dpro 51
52 FFASsuboptimal 46.76 40.22 42.78 -0.77 -0.81 -1.11 46.76 40.22 42.78 -1.12 -1.19 -1.57 FFASsuboptimal 52
53 SAM−T02−server 46.46 40.99 31.24 -0.81 -0.68 -2.51 46.46 40.99 33.38 -1.17 -1.07 -2.92 SAM−T02−server 53
54 3D−JIGSAW_AEP 46.15 39.14 51.25 -0.86 -0.98 -0.08 46.46 39.14 51.25 -1.17 -1.37 -0.36 3D−JIGSAW_AEP 54
55 OLGAFS 46.05 37.95 42.74 -0.87 -1.17 -1.11 46.05 38.73 42.74 -1.23 -1.43 -1.58 OLGAFS 55
56 CpHModels 44.03 38.83 34.39 -1.18 -1.03 -2.13 44.03 38.83 34.39 -1.55 -1.41 -2.77 CpHModels 56
57 FFASstandard 42.71 36.84 31.75 -1.38 -1.34 -2.45 51.11 44.43 47.79 -0.44 -0.53 -0.86 FFASstandard 57
58 BAKER−ROBETTA 42.71 33.60 40.75 -1.38 -1.86 -1.35 57.49 47.50 60.54 0.56 -0.04 0.97 BAKER−ROBETTA 58
59 FFASflextemplate 42.21 37.62 29.15 -1.45 -1.22 -2.76 43.52 39.95 30.61 -1.63 -1.24 -3.31 FFASflextemplate 59
60 rehtnap 40.28 32.66 35.65 -1.75 -2.01 -1.97 47.98 43.73 38.89 -0.93 -0.64 -2.13 rehtnap 60
61 FUGUE_KM 39.07 35.63 29.23 -1.93 -1.54 -2.75 39.07 35.63 29.23 -2.32 -1.92 -3.51 FUGUE_KM 61
62 Distill 37.65 29.55 34.33 -2.14 -2.50 -2.13 40.59 31.78 42.26 -2.08 -2.53 -1.65 Distill 62
63 FOLDpro 26.32 22.87 24.15 -3.86 -3.56 -3.37 33.60 29.22 34.03 -3.18 -2.94 -2.82 FOLDpro 63
64 MUFOLD−MD 11.54 10.90 24.03 -6.09 -5.47 -3.38 11.54 10.90 24.03 -6.62 -5.84 -4.25 MUFOLD−MD 64
65 MUFOLD−Server 11.23 10.76 12.53 -6.14 -5.49 -4.78 12.55 10.76 16.36 -6.47 -5.86 -5.35 MUFOLD−Server 65
66 RBO−Proteus 11.23 9.62 24.16 -6.14 -5.67 -3.37 13.56 11.17 25.12 -6.31 -5.80 -4.10 RBO−Proteus 66
67 RANDOM 10.18 8.97 10.18 -6.30 -5.77 -5.06 10.18 8.97 10.18 -6.84 -6.14 -6.23 RANDOM 67
68 schenk−torda−server 8.40 7.62 9.19 -6.57 -5.99 -5.18 9.62 8.70 9.19 -6.92 -6.19 -6.38 schenk−torda−server 68
69 mahmood−torda−server 7.39 4.89 10.34 -6.72 -6.42 -5.04 8.50 6.65 13.42 -7.10 -6.51 -5.77 mahmood−torda−server 69
70 BHAGEERATH                   -6.30 -5.77 -5.06                   -6.84 -6.14 -6.23 BHAGEERATH 70
71 Pushchino                   -6.30 -5.77 -5.06                   -6.84 -6.14 -6.23 Pushchino 71
72 YASARA                   -6.30 -5.77 -5.06                   -6.84 -6.14 -6.23 YASARA 72
73 huber−torda−server                   -6.30 -5.77 -5.06                   -6.84 -6.14 -6.23 huber−torda−server 73
74 test_http_server_01                   -6.30 -5.77 -5.06                   -0.76 -0.54 -6.23 test_http_server_01 74