T0477

X-ray Targets
387 388 389 390
391 392 393 394
395 396 397 398
399 400 401 402
403 404 405 406
407 408 409 410
411 412 413 414
415 416 417 418
419 420 421 422
423 424 425 426
427 428 429 430
431 432 433 434
435 436 438 439
440 441 442 443
444 445 446 447
448 449 450 451
452 453 454 455
456 457 458 459
461 463 465 470
477 478 479 481
483 485 486 487
488 489 490 491
493 494 495 496
497 501 502 503
504 505 506 507
508 509 510 511
512 513 514

T0477

DEAD-box RNA-helicase DDX52, domain I from Homo sapiens

Target type: Server only

Target sequence:

>T0477 DDX52A, Homo sapiens, 242 residues
SMKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGA

Structure:
Method: X-ray, res=2.1Å, R/Rfree=0.19/0.24
Determined by: SGC
PDB ID: 3dkp

3dkp cartoon
Cartoon diagram of 477: 3dkp. ADP is shown as 'sticks', and Mg as "dots".

PyMOL of 3dkp

Domains:  PyMOL of domains

Single domain from a larger mutidomain protein.

Structure classification:

P-loop-containing nucleoside triphosphate hydrolase fold.

CASP category:

Comparative modeling:medium.

Closest templates:

2db3, 2i4i, 1wrb, 1t6n, 1vec.

Target sequence - PDB file inconsistencies:

T0477    3dkp.pdb    T0477.pdb    PyMOL    PyMOL of domains    

T0477    1 SMKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGA 242
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~|||||||||||||||||||||||||||||||||||||||||||||||||
3dkpA  137 SMKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDG--GFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGA 378

Single domain protein: target 1-191, 194-242 ; pdb 137-327, 330-378

Sequence classification:

DEAD/DEAH box helicase (PF00270) in Pfam.

Server predictions:

T0477:pdb 137-378:seq 1-242:CM_medium;   alignment

distribution of first scores
First models for T0477: 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 #
T0477 T0477 T0477 T0477
First score First Z-score Best score Best Z-score
1 HHpred5 77.81 72.74 78.69 1.54 1.85 1.88 77.81 72.74 78.69 1.33 1.43 1.59 HHpred5 1
2 COMA−M 76.88 71.74 75.27 1.32 1.60 1.17 77.50 73.30 75.52 1.25 1.57 0.93 COMA−M 2
3 METATASSER 76.77 71.01 75.93 1.29 1.41 1.31 76.77 71.01 75.93 1.06 0.98 1.02 METATASSER 3
4 PS2−server 76.46 69.51 74.05 1.21 1.03 0.92 76.46 69.51 74.05 0.97 0.60 0.63 PS2−server 4
5 MULTICOM−RANK 76.35 70.90 75.95 1.19 1.38 1.31 76.35 70.90 75.95 0.94 0.96 1.02 MULTICOM−RANK 5
6 FEIG 76.35 67.40 74.09 1.19 0.49 0.93 76.35 68.89 75.14 0.94 0.44 0.85 FEIG 6
7 Zhang−Server 76.04 70.42 77.65 1.11 1.26 1.66 78.44 74.51 78.28 1.50 1.88 1.51 Zhang−Server 7
8 3D−JIGSAW_AEP 75.94 71.84 73.13 1.09 1.62 0.74 75.94 71.84 73.66 0.84 1.20 0.55 3D−JIGSAW_AEP 8
9 HHpred2 75.94 69.90 74.67 1.09 1.13 1.05 75.94 69.90 74.67 0.84 0.70 0.76 HHpred2 9
10 COMA 75.83 70.07 74.48 1.06 1.17 1.01 75.83 70.07 75.52 0.81 0.74 0.93 COMA 10
11 HHpred4 75.83 67.99 74.83 1.06 0.64 1.08 75.83 67.99 74.83 0.81 0.21 0.79 HHpred4 11
12 MULTICOM−REFINE 75.83 67.01 75.77 1.06 0.39 1.28 75.83 70.14 76.10 0.81 0.76 1.05 MULTICOM−REFINE 12
13 LEE−SERVER 75.73 66.63 77.81 1.04 0.30 1.70 75.73 70.49 78.19 0.78 0.85 1.49 LEE−SERVER 13
14 RAPTOR 75.62 67.71 74.06 1.01 0.57 0.93 75.62 68.85 74.87 0.75 0.43 0.80 RAPTOR 14
15 3D−JIGSAW_V3 75.52 68.16 72.99 0.99 0.69 0.71 75.52 70.03 73.00 0.72 0.73 0.41 3D−JIGSAW_V3 15
16 GS−KudlatyPred 75.42 70.21 73.82 0.97 1.21 0.88 75.42 70.21 73.82 0.70 0.78 0.58 GS−KudlatyPred 16
17 pro−sp3−TASSER 75.31 70.59 75.31 0.94 1.30 1.18 77.29 72.78 77.69 1.19 1.44 1.39 pro−sp3−TASSER 17
18 GS−MetaServer2 75.31 68.72 74.10 0.94 0.83 0.93 75.31 68.72 74.10 0.67 0.40 0.64 GS−MetaServer2 18
19 FAMSD 74.79 70.69 73.74 0.82 1.33 0.86 75.21 70.69 74.17 0.64 0.90 0.65 FAMSD 19
20 MUFOLD−Server 74.79 62.99 72.05 0.82 -0.63 0.51 75.21 67.74 72.05 0.64 0.14 0.21 MUFOLD−Server 20
21 BAKER−ROBETTA 74.69 69.03 70.88 0.79 0.91 0.27 75.00 71.53 73.24 0.59 1.12 0.46 BAKER−ROBETTA 21
22 MUProt 74.69 63.92 75.33 0.79 -0.39 1.19 75.10 70.03 75.95 0.61 0.73 1.02 MUProt 22
23 3DShot2 74.58 66.81 70.90 0.77 0.34 0.28 74.58 66.81 70.90 0.47 -0.09 -0.03 3DShot2 23
24 CpHModels 74.38 66.22 68.86 0.72 0.19 -0.14 74.38 66.22 68.86 0.42 -0.25 -0.45 CpHModels 24
25 MULTICOM−CMFR 74.06 69.90 74.78 0.64 1.13 1.07 75.21 69.90 75.47 0.64 0.70 0.92 MULTICOM−CMFR 25
26 Pushchino 73.75 68.47 69.31 0.57 0.77 -0.05 73.75 68.47 69.31 0.25 0.33 -0.36 Pushchino 26
27 keasar−server 73.75 66.46 72.03 0.57 0.25 0.51 75.42 71.39 72.67 0.70 1.08 0.34 keasar−server 27
28 nFOLD3 73.54 67.36 68.78 0.52 0.48 -0.16 73.54 67.36 71.21 0.20 0.05 0.04 nFOLD3 28
29 Phyre_de_novo 73.33 69.72 74.43 0.47 1.08 1.00 73.33 69.72 74.43 0.14 0.65 0.71 Phyre_de_novo 29
30 Frankenstein 73.23 66.98 74.22 0.44 0.39 0.96 75.62 69.79 74.71 0.75 0.67 0.77 Frankenstein 30
31 3Dpro 72.50 66.18 73.32 0.27 0.18 0.77 72.50 66.18 73.32 -0.08 -0.26 0.48 3Dpro 31
32 MULTICOM−CLUSTER 72.29 66.94 73.88 0.22 0.38 0.89 76.35 70.90 75.95 0.94 0.96 1.02 MULTICOM−CLUSTER 32
33 Fiser−M4T 71.98 67.33 70.78 0.15 0.48 0.25 71.98 67.33 70.78 -0.21 0.04 -0.05 Fiser−M4T 33
34 Pcons_dot_net 71.88 67.29 68.10 0.12 0.47 -0.30 75.42 70.21 74.90 0.70 0.78 0.80 Pcons_dot_net 34
35 Pcons_multi 71.88 67.29 68.10 0.12 0.47 -0.30 77.81 72.67 77.74 1.33 1.41 1.40 Pcons_multi 35
36 ACOMPMOD 71.35 66.49 67.24 -0.00 0.26 -0.47 71.35 66.49 67.24 -0.38 -0.18 -0.79 ACOMPMOD 36
37 circle 71.25 65.21 70.19 -0.03 -0.06 0.13 74.90 69.83 72.47 0.56 0.68 0.30 circle 37
38 huber−torda−server 71.25 64.51 64.79 -0.03 -0.24 -0.97 71.25 64.51 64.79 -0.41 -0.69 -1.30 huber−torda−server 38
39 Pcons_local 70.83 66.94 67.38 -0.13 0.38 -0.44 70.83 66.94 67.38 -0.52 -0.06 -0.76 Pcons_local 39
40 panther_server 70.73 62.81 64.59 -0.15 -0.67 -1.02 70.73 62.81 64.59 -0.55 -1.12 -1.34 panther_server 40
41 GeneSilicoMetaServer 70.10 66.22 65.12 -0.30 0.19 -0.91 71.56 67.12 66.88 -0.33 -0.01 -0.86 GeneSilicoMetaServer 41
42 FUGUE_KM 70.00 65.49 62.60 -0.33 0.01 -1.42 70.00 65.49 62.60 -0.74 -0.43 -1.76 FUGUE_KM 42
43 forecast 69.69 64.34 69.10 -0.40 -0.28 -0.09 69.69 64.34 70.08 -0.82 -0.73 -0.20 forecast 43
44 MUSTER 69.27 65.17 67.99 -0.50 -0.07 -0.32 74.69 66.42 73.24 0.50 -0.19 0.46 MUSTER 44
45 PSI 68.75 61.25 66.67 -0.63 -1.07 -0.59 75.73 67.99 74.72 0.78 0.21 0.77 PSI 45
46 BioSerf 68.75 61.18 67.49 -0.63 -1.09 -0.42 68.75 61.18 67.49 -1.07 -1.54 -0.74 BioSerf 46
47 FFASstandard 67.92 63.19 65.04 -0.82 -0.58 -0.92 67.92 64.86 65.36 -1.29 -0.60 -1.18 FFASstandard 47
48 FFASflextemplate 67.92 63.19 65.04 -0.82 -0.58 -0.92 67.92 63.19 65.04 -1.29 -1.03 -1.25 FFASflextemplate 48
49 Poing 67.71 63.40 65.39 -0.87 -0.52 -0.85 70.52 66.15 68.68 -0.60 -0.26 -0.49 Poing 49
50 Phragment 67.60 63.30 65.24 -0.90 -0.55 -0.88 70.31 65.94 68.91 -0.66 -0.32 -0.44 Phragment 50
51 FFASsuboptimal 67.60 61.35 63.83 -0.90 -1.04 -1.17 67.60 61.35 63.83 -1.38 -1.50 -1.50 FFASsuboptimal 51
52 Phyre2 67.50 63.19 65.36 -0.92 -0.58 -0.86 70.21 65.90 69.11 -0.68 -0.33 -0.40 Phyre2 52
53 SAM−T08−server 67.08 61.11 66.75 -1.02 -1.10 -0.57 67.08 61.11 66.75 -1.51 -1.56 -0.89 SAM−T08−server 53
54 fais−server 66.25 61.39 66.98 -1.22 -1.03 -0.53 75.73 70.45 74.65 0.78 0.84 0.75 fais−server 54
55 SAM−T06−server 65.42 61.32 66.40 -1.42 -1.05 -0.64 66.56 61.32 66.40 -1.65 -1.51 -0.96 SAM−T06−server 55
56 pipe_int 65.42 56.39 67.95 -1.42 -2.30 -0.33 65.42 56.39 67.95 -1.95 -2.77 -0.64 pipe_int 56
57 mariner1 64.90 59.20 60.32 -1.54 -1.59 -1.89 67.08 61.81 65.09 -1.51 -1.38 -1.24 mariner1 57
58 LOOPP_Server 64.48 59.69 62.00 -1.64 -1.47 -1.55 65.83 63.33 62.00 -1.84 -0.99 -1.88 LOOPP_Server 58
59 YASARA 64.27 60.24 64.36 -1.70 -1.33 -1.06 74.27 69.55 72.07 0.39 0.61 0.22 YASARA 59
60 FALCON_CONSENSUS 64.17 57.57 65.45 -1.72 -2.00 -0.84 69.90 61.70 70.27 -0.77 -1.41 -0.16 FALCON_CONSENSUS 60
61 FALCON 64.06 57.60 65.91 -1.75 -2.00 -0.74 69.90 61.70 70.27 -0.77 -1.41 -0.16 FALCON 61
62 Distill 63.96 57.22 59.31 -1.77 -2.09 -2.10 63.96 57.22 59.31 -2.34 -2.56 -2.44 Distill 62
63 mGenTHREADER 63.54 59.51 58.86 -1.87 -1.51 -2.19 63.54 59.51 58.86 -2.45 -1.97 -2.53 mGenTHREADER 63
64 SAM−T02−server 63.33 59.79 60.46 -1.92 -1.44 -1.86 66.56 61.15 62.08 -1.65 -1.55 -1.86 SAM−T02−server 64
65 OLGAFS 61.88 58.54 49.57 -2.27 -1.76 -4.10 61.98 58.54 50.40 -2.87 -2.22 -4.29 OLGAFS 65
66 rehtnap 39.06 30.21 29.34 -7.71 -8.95 -8.24 51.56 43.16 39.77 -5.63 -6.17 -6.51 rehtnap 66
67 FOLDpro 35.52 27.40 34.01 -8.56 -9.67 -7.29 50.52 45.80 47.94 -5.90 -5.49 -4.81 FOLDpro 67
68 MUFOLD−MD 15.42 13.47 30.76 -13.36 -13.21 -7.95 23.85 18.44 33.89 -12.97 -12.53 -7.73 MUFOLD−MD 68
69 RBO−Proteus 14.79 13.75 28.98 -13.51 -13.14 -8.32 15.73 13.85 30.27 -15.13 -13.71 -8.48 RBO−Proteus 69
70 RANDOM 11.95 9.76 11.95 -14.18 -14.15 -11.81 11.95 9.76 11.95 -16.13 -14.76 -12.30 RANDOM 70
71 schenk−torda−server 9.48 8.30 13.87 -14.77 -14.52 -11.42 9.48 8.47 13.87 -16.78 -15.09 -11.90 schenk−torda−server 71
72 mahmood−torda−server 8.96 7.15 13.08 -14.90 -14.81 -11.58 9.79 7.95 14.81 -16.70 -15.22 -11.70 mahmood−torda−server 72
73 BHAGEERATH                   -14.18 -14.15 -11.81                   -16.13 -14.76 -12.30 BHAGEERATH 73
74 test_http_server_01                   -14.18 -14.15 -11.81                   -16.13 -14.76 -12.30 test_http_server_01 74