T0479

X-ray Targets
387 388 389 390
391 392 393 394
395 396 397 398
399 400 401 402
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411 412 413 414
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483 485 486 487
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T0479

Q7W9W5_BORPA from Bordetella parapertussis

Target type: Server only

Target sequence:

>T0479 Q7W9W5_BORPA, Bordetella parapertussis, 134 residues
MSTPHTDFFGLTIPFMQLLGVVPEHSGNGTARTRLPARADLVNSRGDIHGGTLMSVLDFTLGAAIRGDTPEVGVATIDMNTSFMSPGRGDLVIETRCLRRGASIAFCEGEIRDSAGELVAKATATFKIIQRRPG

Structure:
Method: X-ray, res=2.4Å, R/Rfree=0.24/0.26
Determined by: NESG
PDB ID: 3dkz

3dkz_A cartoon
Cartoon diagram of 479: 3dkz chain A

PyMOL of 3dkz

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Thioesterase/thiol ester dehydrase-isomerase fold.

CASP category:

Comparative modeling:easy.

Closest templates:

1zki, 1wlu.

Target sequence - PDB file inconsistencies:

T0479    3dkz.pdb    T0479.pdb    PyMOL    PyMOL of domains    

T0479    1 MSTPHTDFFGLTIPFMQLLGVVPEHSGNGTARTRLPARADLVNSRGDIHGGTLMSVLDFTLGAAIRGDTPEVGVATIDMNTSFMSPGRGDLVIETRCLRRGASIAFCEGEIRDSAGELVAKATATFKIIQRRPG 134
           ~~~~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~
3dkzA   39 -----TDFFGLTIPFMQLLGVVPEHSGNGTARTRLPARADLVNSRGDIHGGTLMSVLDFTLGAAIRGDTPEVGVATIDMNTSFMSPGRGDLVIETRCLRRGASIAFCEGEIRDSAGELVAKATATFKIIQ---- 163

Residue change log: change 49, 87, 112, 117, MSE to MET;

Single domain protein: target 6-130 ; pdb 39-163

Sequence classification:

Thioesterase superfamily (4HBT) in Pfam.

Server predictions:

T0479:pdb 39-163:seq 6-130:CM_easy;   alignment

distribution of first scores
First models for T0479: 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 #
T0479 T0479 T0479 T0479
First score First Z-score Best score Best Z-score
1 Pcons_dot_net 91.40 89.13 87.00 1.01 1.17 1.03 91.40 89.13 87.00 1.11 1.34 1.19 Pcons_dot_net 1
2 Pcons_multi 91.40 89.13 87.00 1.01 1.17 1.03 91.40 89.13 87.00 1.11 1.34 1.19 Pcons_multi 2
3 LEE−SERVER 91.40 83.67 87.14 1.01 0.55 1.05 91.40 88.93 87.70 1.11 1.31 1.35 LEE−SERVER 3
4 FEIG 91.40 81.80 87.00 1.01 0.34 1.03 91.40 84.47 87.00 1.11 0.46 1.19 FEIG 4
5 HHpred2 91.00 81.93 86.50 0.95 0.36 0.96 91.00 81.93 86.50 1.02 -0.02 1.07 HHpred2 5
6 HHpred4 91.00 80.47 85.60 0.95 0.19 0.84 91.00 80.47 85.60 1.02 -0.30 0.86 HHpred4 6
7 HHpred5 90.80 85.60 85.94 0.93 0.77 0.88 90.80 85.60 85.94 0.97 0.67 0.94 HHpred5 7
8 GS−KudlatyPred 90.80 83.07 86.94 0.93 0.49 1.03 90.80 83.07 86.94 0.97 0.19 1.17 GS−KudlatyPred 8
9 RAPTOR 90.60 87.40 86.45 0.90 0.97 0.96 90.60 87.40 86.45 0.93 1.02 1.06 RAPTOR 9
10 FFASstandard 90.40 86.67 85.77 0.87 0.89 0.86 90.40 86.67 85.77 0.88 0.88 0.90 FFASstandard 10
11 FFASsuboptimal 90.40 86.67 85.77 0.87 0.89 0.86 90.40 86.67 85.77 0.88 0.88 0.90 FFASsuboptimal 11
12 YASARA 90.40 86.40 85.99 0.87 0.86 0.89 90.60 88.20 85.99 0.93 1.17 0.95 YASARA 12
13 3D−JIGSAW_V3 90.40 85.07 84.08 0.87 0.71 0.62 90.40 85.07 84.08 0.88 0.57 0.51 3D−JIGSAW_V3 13
14 MUFOLD−Server 90.40 72.13 84.50 0.87 -0.75 0.68 90.40 84.87 84.51 0.88 0.54 0.61 MUFOLD−Server 14
15 Phyre_de_novo 90.20 87.40 87.15 0.84 0.97 1.05 90.20 87.40 87.15 0.84 1.02 1.22 Phyre_de_novo 15
16 circle 90.20 87.27 83.68 0.84 0.96 0.56 90.20 87.27 85.15 0.84 0.99 0.76 circle 16
17 MULTICOM−RANK 90.00 88.40 84.95 0.81 1.09 0.74 90.00 88.40 85.82 0.79 1.21 0.91 MULTICOM−RANK 17
18 MULTICOM−CLUSTER 90.00 88.13 85.48 0.81 1.06 0.82 90.00 88.13 85.48 0.79 1.15 0.83 MULTICOM−CLUSTER 18
19 FFASflextemplate 90.00 87.33 84.00 0.81 0.97 0.61 90.40 87.33 84.02 0.88 1.00 0.50 FFASflextemplate 19
20 BAKER−ROBETTA 90.00 86.40 86.10 0.81 0.86 0.91 91.40 89.13 87.00 1.11 1.34 1.19 BAKER−ROBETTA 20
21 MUProt 89.60 86.93 85.40 0.76 0.92 0.81 89.60 86.93 85.66 0.70 0.93 0.88 MUProt 21
22 FAMSD 89.60 86.67 84.78 0.76 0.89 0.72 89.60 87.20 84.78 0.70 0.98 0.67 FAMSD 22
23 METATASSER 89.40 86.07 83.89 0.73 0.82 0.59 89.40 86.80 83.99 0.66 0.90 0.49 METATASSER 23
24 MULTICOM−REFINE 88.80 84.53 84.98 0.65 0.65 0.75 89.00 85.73 85.70 0.57 0.70 0.89 MULTICOM−REFINE 24
25 3D−JIGSAW_AEP 88.00 85.87 82.09 0.54 0.80 0.34 88.60 86.13 82.62 0.48 0.77 0.18 3D−JIGSAW_AEP 25
26 Pushchino 87.80 85.00 80.36 0.51 0.70 0.10 87.80 85.00 80.36 0.30 0.56 -0.35 Pushchino 26
27 PS2−server 87.80 79.27 84.12 0.51 0.06 0.63 87.80 80.87 84.12 0.30 -0.22 0.52 PS2−server 27
28 huber−torda−server 86.60 83.53 78.20 0.34 0.54 -0.21 86.60 83.53 78.20 0.04 0.28 -0.84 huber−torda−server 28
29 forecast 85.40 79.53 83.36 0.18 0.09 0.52 86.40 80.53 83.55 -0.01 -0.29 0.39 forecast 29
30 3DShot2 85.20 79.07 79.70 0.15 0.03 0.00 85.20 79.07 79.70 -0.27 -0.56 -0.50 3DShot2 30
31 Zhang−Server 85.00 81.80 80.25 0.12 0.34 0.08 87.80 84.07 83.29 0.30 0.38 0.33 Zhang−Server 31
32 PSI 84.80 78.93 79.83 0.09 0.02 0.02 84.80 79.67 79.83 -0.36 -0.45 -0.47 PSI 32
33 pipe_int 84.60 80.60 79.43 0.07 0.21 -0.04 84.60 80.60 79.43 -0.41 -0.27 -0.56 pipe_int 33
34 Fiser−M4T 84.60 78.60 79.28 0.07 -0.02 -0.06 84.60 78.60 79.28 -0.41 -0.65 -0.59 Fiser−M4T 34
35 COMA 84.40 80.00 79.88 0.04 0.14 0.03 90.80 84.93 86.12 0.97 0.55 0.98 COMA 35
36 SAM−T08−server 84.00 82.13 81.08 -0.02 0.38 0.20 90.60 84.33 84.88 0.93 0.43 0.70 SAM−T08−server 36
37 fais−server 83.60 78.27 79.74 -0.07 -0.06 0.01 90.80 83.20 86.18 0.97 0.22 1.00 fais−server 37
38 COMA−M 83.60 72.80 79.24 -0.07 -0.67 -0.06 89.20 86.27 84.37 0.62 0.80 0.58 COMA−M 38
39 SAM−T06−server 83.20 78.93 79.68 -0.13 0.02 -0.00 83.20 79.07 79.68 -0.72 -0.56 -0.50 SAM−T06−server 39
40 pro−sp3−TASSER 83.00 79.00 78.28 -0.16 0.03 -0.20 90.20 86.93 83.24 0.84 0.93 0.32 pro−sp3−TASSER 40
41 Pcons_local 83.00 77.93 79.27 -0.16 -0.09 -0.06 83.00 78.60 79.27 -0.76 -0.65 -0.60 Pcons_local 41
42 MULTICOM−CMFR 82.80 78.13 80.88 -0.18 -0.07 0.17 83.80 80.47 81.05 -0.59 -0.30 -0.19 MULTICOM−CMFR 42
43 MUSTER 82.80 77.07 79.44 -0.18 -0.19 -0.03 83.80 79.93 81.65 -0.59 -0.40 -0.05 MUSTER 43
44 GS−MetaServer2 82.60 80.60 78.08 -0.21 0.21 -0.23 89.60 80.60 84.02 0.70 -0.27 0.50 GS−MetaServer2 44
45 BioSerf 82.20 79.53 79.06 -0.27 0.09 -0.09 82.20 79.53 79.06 -0.94 -0.48 -0.64 BioSerf 45
46 nFOLD3 82.20 79.40 76.57 -0.27 0.07 -0.44 82.80 79.40 78.89 -0.81 -0.50 -0.68 nFOLD3 46
47 GeneSilicoMetaServer 82.20 77.93 78.94 -0.27 -0.09 -0.10 83.80 79.73 79.25 -0.59 -0.44 -0.60 GeneSilicoMetaServer 47
48 Frankenstein 82.00 79.47 77.78 -0.30 0.08 -0.27 85.20 81.73 80.57 -0.27 -0.06 -0.30 Frankenstein 48
49 panther_server 81.80 77.40 75.17 -0.32 -0.15 -0.64 82.00 78.27 79.73 -0.99 -0.72 -0.49 panther_server 49
50 keasar−server 81.80 75.93 77.09 -0.32 -0.32 -0.37 82.80 79.07 78.72 -0.81 -0.56 -0.72 keasar−server 50
51 CpHModels 81.40 75.40 78.08 -0.38 -0.38 -0.23 81.40 75.40 78.08 -1.12 -1.26 -0.87 CpHModels 51
52 mGenTHREADER 81.00 78.33 75.79 -0.43 -0.05 -0.55 81.00 78.33 75.79 -1.21 -0.71 -1.40 mGenTHREADER 52
53 SAM−T02−server 79.40 75.53 80.35 -0.66 -0.36 0.09 83.40 81.53 80.53 -0.67 -0.10 -0.31 SAM−T02−server 53
54 FALCON 78.80 70.53 76.41 -0.74 -0.93 -0.46 78.80 70.53 76.41 -1.70 -2.19 -1.26 FALCON 54
55 3Dpro 78.60 74.47 75.86 -0.77 -0.48 -0.54 78.60 74.47 75.86 -1.74 -1.44 -1.38 3Dpro 55
56 Poing 78.00 72.13 74.95 -0.85 -0.75 -0.67 83.00 80.93 78.84 -0.76 -0.21 -0.70 Poing 56
57 Phyre2 78.00 72.13 74.95 -0.85 -0.75 -0.67 83.20 81.47 77.89 -0.72 -0.11 -0.91 Phyre2 57
58 Phragment 78.00 72.13 74.95 -0.85 -0.75 -0.67 83.20 81.47 77.87 -0.72 -0.11 -0.92 Phragment 58
59 ACOMPMOD 78.00 71.20 72.09 -0.85 -0.85 -1.07 78.00 71.20 72.09 -1.88 -2.06 -2.25 ACOMPMOD 59
60 Distill 77.00 70.73 69.67 -0.99 -0.91 -1.41 77.00 70.73 69.67 -2.10 -2.15 -2.81 Distill 60
61 rehtnap 66.40 52.27 58.56 -2.46 -2.99 -2.98 66.40 55.27 58.90 -4.46 -5.08 -5.29 rehtnap 61
62 FUGUE_KM 65.20 54.67 55.55 -2.63 -2.72 -3.41 71.20 62.53 58.36 -3.39 -3.70 -5.42 FUGUE_KM 62
63 MUFOLD−MD 59.60 44.07 62.87 -3.41 -3.91 -2.37 61.60 50.67 62.87 -5.52 -5.95 -4.38 MUFOLD−MD 63
64 OLGAFS 57.60 52.80 44.10 -3.68 -2.93 -5.03 58.40 54.93 44.26 -6.24 -5.14 -8.67 OLGAFS 64
65 LOOPP_Server 56.20 43.00 48.30 -3.88 -4.03 -4.43 83.80 80.07 79.88 -0.59 -0.38 -0.46 LOOPP_Server 65
66 FOLDpro 49.60 37.73 47.03 -4.79 -4.63 -4.61 65.00 60.87 67.44 -4.77 -4.02 -3.32 FOLDpro 66
67 FALCON_CONSENSUS 48.80 41.60 54.12 -4.91 -4.19 -3.61 78.80 70.53 76.41 -1.70 -2.19 -1.26 FALCON_CONSENSUS 67
68 mariner1 44.80 41.47 38.74 -5.46 -4.21 -5.78 85.40 82.87 79.92 -0.23 0.16 -0.45 mariner1 68
69 RBO−Proteus 36.20 29.13 44.95 -6.65 -5.60 -4.91 42.40 35.40 50.39 -9.79 -8.85 -7.25 RBO−Proteus 69
70 RANDOM 16.98 13.75 16.98 -9.32 -7.33 -8.86 16.98 13.75 16.98 -15.45 -12.96 -14.95 RANDOM 70
71 mahmood−torda−server 16.20 11.13 20.48 -9.43 -7.63 -8.36 16.20 11.67 23.12 -15.62 -13.35 -13.54 mahmood−torda−server 71
72 schenk−torda−server 14.00 11.40 18.65 -9.74 -7.60 -8.62 16.80 14.47 18.65 -15.49 -12.82 -14.57 schenk−torda−server 72
73 BHAGEERATH                   -9.32 -7.33 -8.86                   -15.45 -12.96 -14.95 BHAGEERATH 73
74 test_http_server_01                   -9.32 -7.33 -8.86                   -15.45 -12.96 -14.95 test_http_server_01 74