T0420

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

T0420

protein Q97W15_SULSO from Sulfolobus solfataricus

Target type: Server only

Target sequence:

>T0420 Q97W15_SULSO, Sulfolobus solfataricus, 189 residues
MNIGVIILAAGEGKRFGGDKLLAKIDNTPIIMRTIRIYGDLEKIIIVGKYVNEMLPLLMDQIVIYNPFWNEGISTSLKLGLRFFKDYDAVLVALGDMPFVTKEDVNKIINTFKPNCKAVIPTHKGERGNPVLISKSLFNEIEKLRGDVGARVILNKIKIEELCFIECSEGVLIDIDKKEDLMRLRDFHP

Structure:
Method: X-ray, res=2.8Å, R/Rfree=0.23/0.27
Determined by: NESG
PDB ID: 3d5n

3d5n_A cartoon
Cartoon diagram of 420: 3d5n chain A

PyMOL of 3d5n

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Nucleotide-diphospho-sugar transferase fold and superfamily.

CASP category:

Comparative modeling:hard.

Closest templates:

1vic, 1h7e, 1vh1.

Target sequence - PDB file inconsistencies:

T0420    3d5n.pdb    T0420.pdb    PyMOL    PyMOL of domains    

T0420    1 MNIGVIILAAGEGKRFGGDKLLAKIDNTPIIMRTIRIYGDLEKIIIVGKYVNEMLPLLMDQIVIYNPFWNEGISTSLKLGLRFFKDYDAVLVALGDMPFVTKEDVNKIINTFKPNCKAVIPTHKGERGNPVLISKSLFNEIEKLRGDVGARVILNKIKIEELCFIECSEGVLIDIDKKEDLMRLRDFHP 189
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~~~~~~
3d5nA    1 MNIGVIILAAGEGKRFGGDKLLAKIDNTPIIMRTIRIYGDLEKIIIVGKYVNEMLPLLMDQIVIYNPFWNEGISTSLKLGLRFFKDYDAVLVALGDMPFVTKEDVNKIINTFKPNCKAVIPTHKGERGNPVLISKSLFNEIEKLRGDVGARVILNKIKIEELCFIECSEGVLIDIDKK----------- 178

Residue change log: change 1, 32, 54, 59, 97, MSE to MET;

Single domain protein: target 1-178 ; pdb 1-178

Sequence classification:

Uncharacterized protein family UPF0007 (IspD) in Pfam.

Server predictions:

T0420:pdb 1-178:seq 1-178:CM_hard;   alignment

distribution of first scores
First models for T0420: 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 #
T0420 T0420 T0420 T0420
First score First Z-score Best score Best Z-score
1 METATASSER 68.12 59.78 59.94 2.21 2.05 2.06 68.12 59.78 59.94 1.53 1.34 1.40 METATASSER 1
2 forecast 67.84 60.44 59.75 2.15 2.17 2.02 67.84 60.44 59.75 1.48 1.46 1.36 forecast 2
3 RAPTOR 67.84 58.29 59.95 2.15 1.77 2.06 69.24 63.34 62.66 1.75 2.00 1.88 RAPTOR 3
4 Phyre_de_novo 67.70 61.80 61.22 2.12 2.42 2.29 67.70 61.80 61.22 1.45 1.71 1.62 Phyre_de_novo 4
5 circle 65.17 58.90 56.40 1.62 1.89 1.42 65.17 58.90 56.40 0.96 1.17 0.77 circle 5
6 FEIG 64.19 56.13 56.52 1.42 1.37 1.44 69.66 63.67 61.12 1.83 2.06 1.61 FEIG 6
7 BioSerf 64.05 57.68 54.43 1.39 1.66 1.06 64.05 57.68 54.43 0.74 0.94 0.42 BioSerf 7
8 MUProt 63.76 56.18 56.24 1.33 1.38 1.39 63.76 56.18 56.24 0.68 0.66 0.74 MUProt 8
9 LEE−SERVER 63.62 57.54 57.86 1.31 1.63 1.68 65.03 58.85 57.96 0.93 1.16 1.04 LEE−SERVER 9
10 GS−KudlatyPred 63.62 53.70 55.23 1.31 0.93 1.20 63.62 53.70 55.23 0.66 0.20 0.56 GS−KudlatyPred 10
11 SAM−T08−server 63.48 55.71 53.03 1.28 1.30 0.81 63.48 55.71 53.03 0.63 0.58 0.17 SAM−T08−server 11
12 MULTICOM−CLUSTER 62.08 54.87 55.15 1.00 1.14 1.19 63.62 55.76 55.15 0.66 0.59 0.54 MULTICOM−CLUSTER 12
13 MULTICOM−REFINE 62.08 54.40 54.43 1.00 1.06 1.06 62.64 54.40 54.43 0.47 0.33 0.42 MULTICOM−REFINE 13
14 LOOPP_Server 61.94 54.07 51.41 0.97 0.99 0.51 70.51 61.14 60.02 1.99 1.59 1.41 LOOPP_Server 14
15 HHpred5 61.52 55.52 53.41 0.89 1.26 0.87 61.52 55.52 53.41 0.25 0.54 0.23 HHpred5 15
16 COMA−M 61.38 53.14 51.63 0.86 0.82 0.55 61.38 53.14 51.63 0.22 0.10 -0.08 COMA−M 16
17 3DShot2 60.81 50.14 51.39 0.75 0.27 0.51 60.81 50.14 51.39 0.11 -0.46 -0.12 3DShot2 17
18 mGenTHREADER 60.53 54.63 48.64 0.69 1.10 0.01 60.53 54.63 48.64 0.06 0.38 -0.61 mGenTHREADER 18
19 Zhang−Server 59.83 51.12 52.10 0.55 0.45 0.64 59.83 51.26 52.17 -0.08 -0.25 0.01 Zhang−Server 19
20 FUGUE_KM 59.41 52.39 50.01 0.47 0.68 0.26 60.53 52.67 50.15 0.06 0.01 -0.35 FUGUE_KM 20
21 SAM−T06−server 58.71 49.53 50.25 0.33 0.16 0.30 65.31 56.04 53.15 0.98 0.64 0.19 SAM−T06−server 21
22 HHpred4 58.43 47.57 55.65 0.27 -0.20 1.28 58.43 47.57 55.65 -0.35 -0.94 0.63 HHpred4 22
23 keasar−server 57.87 48.13 47.03 0.16 -0.10 -0.28 62.08 55.90 52.01 0.36 0.61 -0.01 keasar−server 23
24 ACOMPMOD 57.16 49.48 49.43 0.02 0.15 0.15 57.16 50.84 49.83 -0.60 -0.33 -0.40 ACOMPMOD 24
25 FOLDpro 57.16 46.96 46.13 0.02 -0.32 -0.45 57.16 46.96 46.13 -0.60 -1.05 -1.06 FOLDpro 25
26 Pushchino 56.74 47.47 44.74 -0.07 -0.22 -0.70 56.74 47.47 44.74 -0.68 -0.96 -1.31 Pushchino 26
27 GeneSilicoMetaServer 56.74 46.54 46.48 -0.07 -0.39 -0.38 62.64 54.77 53.65 0.47 0.40 0.28 GeneSilicoMetaServer 27
28 FALCON_CONSENSUS 56.74 44.66 47.99 -0.07 -0.74 -0.11 64.33 56.65 55.15 0.79 0.75 0.54 FALCON_CONSENSUS 28
29 FALCON 56.74 44.66 47.99 -0.07 -0.74 -0.11 64.33 56.65 55.15 0.79 0.75 0.54 FALCON 29
30 Pcons_local 56.32 48.27 47.80 -0.15 -0.07 -0.14 60.11 50.47 52.14 -0.03 -0.40 0.01 Pcons_local 30
31 Pcons_dot_net 56.32 45.27 47.54 -0.15 -0.63 -0.19 61.52 52.90 54.23 0.25 0.05 0.38 Pcons_dot_net 31
32 Pcons_multi 56.32 45.27 47.54 -0.15 -0.63 -0.19 61.38 54.26 52.26 0.22 0.31 0.03 Pcons_multi 32
33 COMA 56.18 48.41 47.35 -0.18 -0.05 -0.22 57.16 48.41 51.63 -0.60 -0.78 -0.08 COMA 33
34 3Dpro 56.04 47.14 45.10 -0.21 -0.28 -0.63 56.04 47.14 47.52 -0.82 -1.02 -0.81 3Dpro 34
35 fais−server 55.90 47.19 51.25 -0.23 -0.27 0.48 59.97 50.42 56.08 -0.05 -0.41 0.71 fais−server 35
36 FFASstandard 55.62 48.41 48.35 -0.29 -0.05 -0.04 55.62 48.41 48.77 -0.90 -0.78 -0.59 FFASstandard 36
37 BAKER−ROBETTA 55.48 48.64 50.89 -0.32 -0.01 0.42 55.62 48.64 50.89 -0.90 -0.74 -0.21 BAKER−ROBETTA 37
38 PSI 55.48 46.49 50.81 -0.32 -0.40 0.40 64.05 57.77 56.89 0.74 0.96 0.85 PSI 38
39 MUSTER 55.34 47.66 47.09 -0.35 -0.19 -0.27 62.50 54.73 58.26 0.44 0.39 1.10 MUSTER 39
40 MULTICOM−RANK 55.20 46.11 45.13 -0.37 -0.47 -0.63 62.36 54.31 55.20 0.41 0.32 0.55 MULTICOM−RANK 40
41 FFASsuboptimal 55.06 47.75 48.77 -0.40 -0.17 0.03 55.62 48.13 48.95 -0.90 -0.84 -0.56 FFASsuboptimal 41
42 pro−sp3−TASSER 54.92 50.14 44.65 -0.43 0.27 -0.71 67.98 62.55 56.99 1.50 1.85 0.87 pro−sp3−TASSER 42
43 pipe_int 54.92 46.02 44.52 -0.43 -0.49 -0.74 63.76 57.30 54.91 0.68 0.87 0.50 pipe_int 43
44 PS2−server 54.92 44.34 46.56 -0.43 -0.80 -0.37 65.87 58.47 58.96 1.09 1.09 1.22 PS2−server 44
45 HHpred2 54.77 44.94 46.25 -0.46 -0.69 -0.42 54.77 44.94 46.25 -1.06 -1.43 -1.04 HHpred2 45
46 FFASflextemplate 54.63 46.40 48.66 -0.49 -0.42 0.01 55.34 48.41 48.93 -0.95 -0.78 -0.56 FFASflextemplate 46
47 CpHModels 54.49 47.38 47.95 -0.52 -0.24 -0.12 54.49 47.38 47.95 -1.12 -0.98 -0.74 CpHModels 47
48 YASARA 54.49 46.72 45.11 -0.52 -0.36 -0.63 55.76 48.27 47.67 -0.87 -0.81 -0.79 YASARA 48
49 FAMSD 54.21 43.21 46.08 -0.57 -1.01 -0.45 54.92 47.24 46.08 -1.03 -1.00 -1.07 FAMSD 49
50 Phyre2 53.65 45.13 46.17 -0.68 -0.65 -0.44 62.92 54.96 56.39 0.52 0.44 0.76 Phyre2 50
51 Poing 53.65 44.29 46.37 -0.68 -0.81 -0.40 62.92 55.15 55.98 0.52 0.47 0.69 Poing 51
52 Phragment 53.65 44.29 46.37 -0.68 -0.81 -0.40 62.92 54.96 56.39 0.52 0.44 0.76 Phragment 52
53 SAM−T02−server 53.23 43.12 46.17 -0.77 -1.02 -0.44 53.23 44.57 46.17 -1.36 -1.50 -1.05 SAM−T02−server 53
54 GS−MetaServer2 52.11 45.83 40.56 -0.99 -0.53 -1.45 57.58 48.13 51.79 -0.52 -0.84 -0.05 GS−MetaServer2 54
55 3D−JIGSAW_AEP 50.98 46.77 39.02 -1.22 -0.35 -1.73 51.40 47.00 39.02 -1.72 -1.05 -2.32 3D−JIGSAW_AEP 55
56 MUFOLD−Server 50.70 38.67 44.21 -1.27 -1.85 -0.79 50.70 38.67 44.21 -1.85 -2.60 -1.40 MUFOLD−Server 56
57 nFOLD3 50.28 40.17 37.40 -1.36 -1.57 -2.03 51.83 46.16 41.40 -1.63 -1.20 -1.90 nFOLD3 57
58 MULTICOM−CMFR 49.30 42.27 43.57 -1.55 -1.18 -0.91 55.62 50.84 49.22 -0.90 -0.33 -0.51 MULTICOM−CMFR 58
59 3D−JIGSAW_V3 48.88 46.16 37.78 -1.64 -0.46 -1.96 49.58 46.96 37.78 -2.07 -1.05 -2.54 3D−JIGSAW_V3 59
60 panther_server 47.75 38.48 37.43 -1.86 -1.88 -2.02 51.97 44.29 39.33 -1.61 -1.55 -2.27 panther_server 60
61 Distill 46.91 37.92 41.08 -2.03 -1.98 -1.36 47.75 39.89 41.08 -2.42 -2.37 -1.96 Distill 61
62 Fiser−M4T 46.77 40.78 37.01 -2.06 -1.46 -2.10 46.77 40.78 37.01 -2.61 -2.21 -2.68 Fiser−M4T 62
63 rehtnap 38.06 31.04 28.73 -3.80 -3.25 -3.60 47.19 37.17 35.38 -2.53 -2.88 -2.97 rehtnap 63
64 mariner1 29.07 23.64 24.99 -5.59 -4.62 -4.28 64.61 57.87 60.48 0.85 0.98 1.49 mariner1 64
65 MUFOLD−MD 19.94 17.79 28.43 -7.42 -5.70 -3.65 21.91 18.54 28.43 -7.44 -6.35 -4.21 MUFOLD−MD 65
66 RBO−Proteus 15.73 13.34 24.61 -8.26 -6.52 -4.34 17.27 15.26 27.27 -8.34 -6.96 -4.41 RBO−Proteus 66
67 RANDOM 12.54 10.51 12.54 -8.89 -7.04 -6.53 12.54 10.51 12.54 -9.26 -7.85 -7.03 RANDOM 67
68 schenk−torda−server 11.66 10.16 12.93 -9.07 -7.10 -6.46 13.20 11.42 13.08 -9.13 -7.68 -6.94 schenk−torda−server 68
69 OLGAFS 10.67 8.85 3.89 -9.27 -7.35 -8.10 10.96 9.36 4.05 -9.57 -8.06 -8.54 OLGAFS 69
70 mahmood−torda−server 10.39 9.41 14.80 -9.32 -7.24 -6.12 10.67 10.02 14.80 -9.62 -7.94 -6.63 mahmood−torda−server 70
71 BHAGEERATH                   -8.89 -7.04 -6.53                   -9.26 -7.85 -7.03 BHAGEERATH 71
72 Frankenstein                   -8.89 -7.04 -6.53                   -9.26 -7.85 -7.03 Frankenstein 72
73 huber−torda−server                   -8.89 -7.04 -6.53                   -9.26 -7.85 -7.03 huber−torda−server 73
74 test_http_server_01                   -8.89 -7.04 -6.53                   -9.26 -7.85 -7.03 test_http_server_01 74