T0502

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
435 436 437 438
439 440 441 442
443 444 445 446
447 448 449 450
451 452 453 454
455 456 457 458
459 460 461 462
463 464 465 466
467 468 469 470
471 472 473 474
475 476 477 478
479 480 481 482
483 484 485 486
487 488 489 490
491 492 493 494
495 496 497 498
499 500 501 502
503 504 505 506
507 508 509 510
511 512 513 514

T0502

domain of a replication factor A protein from Methanocaldococcus jannaschii

Target type: Server only

Target sequence:

>T0502 MjR118E, Methanocaldococcus jannaschii, 105 residues
EIKDTYNIGELSPGMTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTDIDVGRGDYVRVRGYIREGYYGGLECTANYVEILKKGEKIES

Structure:
Method: X-ray, res=2.4Å, R/Rfree=0.23/0.27
Determined by: NESG
PDB ID: 3dm3

3dm3_A cartoon
Cartoon diagram of 502: 3dm3 chain A

PyMOL of 3dm3

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

OB fold.

CASP category:

Comparative modeling:medium.

Closest templates:

1o7i.

Target sequence - PDB file inconsistencies:

T0502    3dm3.pdb    T0502.pdb    PyMOL    PyMOL of domains    

T0502    1 EIKDTYNIGELSPGMTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTDIDVGRGDYVRVRGYIREGYYGGLECTANYVEILKKGEKIES 105
           ~~~||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~
3dm3A    4 ---DTYNIGELSPGMTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTDIDVGRGDYVRVRGYIREGYYGGLECTANYVEILKKGE---- 101

Single domain protein: target 4-101 ; pdb 4-101

Sequence classification:

OB-fold nucleic acid binding domain (tRNA_anti) in Pfam.

Server predictions:

T0502:pdb 4-101:seq 4-101:CM_medium;   alignment

distribution of first scores
First models for T0502: 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 #
T0502 T0502 T0502 T0502
First score First Z-score Best score Best Z-score
1 METATASSER 79.34 72.36 76.61 2.78 2.30 1.39 80.36 73.04 76.61 2.92 2.47 0.86 METATASSER 1
2 3D−JIGSAW_V3 76.02 70.75 79.10 1.73 1.91 2.06 77.30 70.75 79.10 1.75 1.72 1.55 3D−JIGSAW_V3 2
3 HHpred4 75.77 69.30 77.89 1.65 1.56 1.73 75.77 69.30 77.89 1.16 1.25 1.21 HHpred4 3
4 HHpred5 75.77 69.30 77.89 1.65 1.56 1.73 75.77 69.30 77.89 1.16 1.25 1.21 HHpred5 4
5 pro−sp3−TASSER 75.51 69.05 73.60 1.57 1.50 0.58 80.87 73.89 76.85 3.12 2.75 0.92 pro−sp3−TASSER 5
6 Phyre_de_novo 74.75 69.64 74.11 1.33 1.64 0.72 74.75 69.64 74.11 0.77 1.36 0.17 Phyre_de_novo 6
7 FFASsuboptimal 74.23 67.09 75.88 1.17 1.02 1.19 74.23 67.09 75.88 0.57 0.53 0.66 FFASsuboptimal 7
8 LEE−SERVER 74.23 65.22 73.91 1.17 0.57 0.67 77.30 68.96 75.20 1.75 1.14 0.47 LEE−SERVER 8
9 Zhang−Server 73.98 66.50 75.61 1.09 0.88 1.12 77.81 70.49 79.58 1.94 1.64 1.68 Zhang−Server 9
10 Pcons_dot_net 73.47 65.65 72.37 0.93 0.68 0.25 73.47 65.65 72.37 0.28 0.06 -0.31 Pcons_dot_net 10
11 Pcons_multi 73.21 65.73 78.59 0.85 0.69 1.92 73.47 65.73 78.59 0.28 0.09 1.41 Pcons_multi 11
12 Pushchino 73.21 64.88 73.19 0.85 0.49 0.47 73.21 64.88 73.19 0.18 -0.19 -0.09 Pushchino 12
13 CpHModels 72.70 67.09 74.32 0.68 1.02 0.78 72.70 67.09 74.32 -0.01 0.53 0.23 CpHModels 13
14 RAPTOR 72.70 64.88 71.51 0.68 0.49 0.02 72.70 64.88 71.51 -0.01 -0.19 -0.55 RAPTOR 14
15 3Dpro 72.45 63.09 72.04 0.61 0.05 0.16 72.45 63.09 72.04 -0.11 -0.77 -0.40 3Dpro 15
16 MULTICOM−CMFR 72.19 65.05 70.54 0.52 0.53 -0.24 75.51 69.56 73.82 1.06 1.34 0.09 MULTICOM−CMFR 16
17 Frankenstein 72.19 64.88 73.93 0.52 0.49 0.67 72.19 65.48 73.93 -0.21 0.01 0.12 Frankenstein 17
18 MUSTER 72.19 64.37 73.27 0.52 0.36 0.49 77.04 68.28 77.59 1.65 0.92 1.13 MUSTER 18
19 FFASstandard 72.19 63.52 72.60 0.52 0.16 0.31 72.19 63.52 72.60 -0.21 -0.63 -0.25 FFASstandard 19
20 MUProt 72.19 63.01 73.79 0.52 0.03 0.63 73.72 65.65 74.07 0.38 0.06 0.16 MUProt 20
21 PS2−server 72.19 58.42 73.91 0.52 -1.08 0.67 72.19 62.92 73.91 -0.21 -0.83 0.11 PS2−server 21
22 fais−server 71.94 63.95 72.27 0.44 0.26 0.23 71.94 63.95 72.53 -0.30 -0.49 -0.27 fais−server 22
23 MULTICOM−REFINE 71.94 63.60 73.52 0.44 0.18 0.56 73.21 65.22 74.35 0.18 -0.08 0.23 MULTICOM−REFINE 23
24 BioSerf 71.68 64.54 67.45 0.36 0.41 -1.07 71.68 64.54 67.45 -0.40 -0.30 -1.67 BioSerf 24
25 HHpred2 71.68 62.16 73.01 0.36 -0.17 0.42 71.68 62.16 73.01 -0.40 -1.08 -0.14 HHpred2 25
26 FAMSD 71.43 66.67 72.57 0.28 0.92 0.31 71.43 66.67 72.57 -0.50 0.39 -0.26 FAMSD 26
27 ACOMPMOD 71.17 62.16 73.32 0.20 -0.17 0.51 71.17 62.16 73.32 -0.60 -1.08 -0.05 ACOMPMOD 27
28 COMA 70.92 66.84 71.92 0.12 0.96 0.13 71.43 66.84 72.51 -0.50 0.45 -0.27 COMA 28
29 3D−JIGSAW_AEP 70.92 63.78 69.35 0.12 0.22 -0.56 70.92 64.03 69.35 -0.69 -0.47 -1.15 3D−JIGSAW_AEP 29
30 3DShot2 70.92 63.44 70.55 0.12 0.14 -0.24 70.92 63.44 70.55 -0.69 -0.66 -0.82 3DShot2 30
31 FFASflextemplate 70.41 63.44 71.67 -0.04 0.14 0.06 71.43 63.86 71.80 -0.50 -0.52 -0.47 FFASflextemplate 31
32 FEIG 70.41 62.59 75.21 -0.04 -0.07 1.01 74.23 68.45 79.35 0.57 0.97 1.62 FEIG 32
33 PSI 70.41 62.59 70.26 -0.04 -0.07 -0.31 72.19 67.26 72.23 -0.21 0.59 -0.35 PSI 33
34 panther_server 70.41 62.41 69.65 -0.04 -0.11 -0.48 70.41 62.41 69.65 -0.89 -1.00 -1.07 panther_server 34
35 COMA−M 70.15 64.37 70.84 -0.12 0.36 -0.16 73.47 67.01 72.51 0.28 0.50 -0.27 COMA−M 35
36 SAM−T08−server 70.15 64.03 71.71 -0.12 0.28 0.08 71.94 64.54 76.07 -0.30 -0.30 0.71 SAM−T08−server 36
37 Fiser−M4T 70.15 62.50 74.92 -0.12 -0.09 0.94 70.15 62.50 74.92 -0.99 -0.97 0.39 Fiser−M4T 37
38 Pcons_local 69.90 65.48 71.41 -0.20 0.63 -0.01 75.00 70.07 78.71 0.87 1.50 1.44 Pcons_local 38
39 keasar−server 69.90 64.80 66.59 -0.20 0.47 -1.30 70.92 64.80 69.77 -0.69 -0.22 -1.03 keasar−server 39
40 huber−torda−server 69.90 64.12 70.13 -0.20 0.30 -0.35 69.90 64.12 70.13 -1.08 -0.44 -0.93 huber−torda−server 40
41 GS−MetaServer2 69.90 63.44 71.16 -0.20 0.14 -0.07 71.43 64.46 71.60 -0.50 -0.33 -0.53 GS−MetaServer2 41
42 FUGUE_KM 69.90 62.76 70.17 -0.20 -0.03 -0.34 69.90 62.76 70.17 -1.08 -0.88 -0.92 FUGUE_KM 42
43 LOOPP_Server 69.64 57.74 73.36 -0.28 -1.24 0.52 72.70 66.41 77.61 -0.01 0.31 1.14 LOOPP_Server 43
44 nFOLD3 68.88 61.91 69.41 -0.52 -0.23 -0.54 74.49 66.50 78.44 0.67 0.34 1.36 nFOLD3 44
45 GS−KudlatyPred 68.88 55.78 71.23 -0.52 -1.72 -0.05 73.98 64.97 73.82 0.48 -0.16 0.09 GS−KudlatyPred 45
46 MUFOLD−Server 68.62 60.80 70.22 -0.60 -0.50 -0.32 70.15 62.33 72.64 -0.99 -1.02 -0.24 MUFOLD−Server 46
47 MULTICOM−RANK 68.62 60.63 71.27 -0.60 -0.54 -0.04 73.47 67.86 72.59 0.28 0.78 -0.25 MULTICOM−RANK 47
48 MULTICOM−CLUSTER 68.62 60.63 71.27 -0.60 -0.54 -0.04 75.77 64.12 81.46 1.16 -0.44 2.20 MULTICOM−CLUSTER 48
49 circle 68.62 56.55 68.49 -0.60 -1.53 -0.79 73.21 68.62 76.52 0.18 1.03 0.83 circle 49
50 Phyre2 68.37 63.27 71.17 -0.68 0.10 -0.07 72.19 65.05 72.14 -0.21 -0.13 -0.38 Phyre2 50
51 GeneSilicoMetaServer 68.37 60.54 71.60 -0.68 -0.56 0.05 72.19 66.58 72.23 -0.21 0.36 -0.35 GeneSilicoMetaServer 51
52 BAKER−ROBETTA 68.11 64.71 70.47 -0.76 0.45 -0.26 72.19 64.71 75.57 -0.21 -0.25 0.57 BAKER−ROBETTA 52
53 Phragment 68.11 63.01 71.03 -0.76 0.03 -0.11 72.19 65.05 72.14 -0.21 -0.13 -0.38 Phragment 53
54 Poing 67.86 62.76 71.11 -0.84 -0.03 -0.09 72.19 64.88 72.59 -0.21 -0.19 -0.25 Poing 54
55 mGenTHREADER 67.09 60.80 61.83 -1.09 -0.50 -2.58 67.09 60.80 61.83 -2.16 -1.52 -3.23 mGenTHREADER 55
56 pipe_int 67.09 58.93 64.48 -1.09 -0.95 -1.87 67.09 58.93 64.48 -2.16 -2.13 -2.49 pipe_int 56
57 FOLDpro 66.33 53.40 66.18 -1.33 -2.30 -1.41 72.45 63.09 72.04 -0.11 -0.77 -0.40 FOLDpro 57
58 forecast 66.07 53.83 69.38 -1.41 -2.19 -0.55 72.96 68.20 75.86 0.09 0.89 0.65 forecast 58
59 SAM−T02−server 65.82 53.57 65.39 -1.49 -2.25 -1.62 65.82 55.87 66.67 -2.64 -3.13 -1.89 SAM−T02−server 59
60 SAM−T06−server 65.56 55.78 69.19 -1.57 -1.72 -0.60 67.86 59.35 69.19 -1.86 -1.99 -1.19 SAM−T06−server 60
61 rehtnap 55.87 50.26 52.88 -4.63 -3.06 -4.98 55.87 50.26 52.88 -6.45 -4.96 -5.70 rehtnap 61
62 FALCON_CONSENSUS 54.34 47.36 55.47 -5.11 -3.76 -4.28 54.34 47.36 56.24 -7.04 -5.90 -4.77 FALCON_CONSENSUS 62
63 FALCON 54.34 47.36 55.47 -5.11 -3.76 -4.28 54.34 47.36 56.24 -7.04 -5.90 -4.77 FALCON 63
64 Distill 49.49 42.01 48.19 -6.64 -5.06 -6.24 56.63 48.13 51.58 -6.16 -5.65 -6.06 Distill 64
65 mariner1 36.48 32.40 24.16 -10.75 -7.39 -12.69 76.28 67.94 80.31 1.36 0.81 1.88 mariner1 65
66 RBO−Proteus 34.18 30.61 45.19 -11.47 -7.82 -7.04 35.71 33.67 45.19 -14.17 -10.37 -7.83 RBO−Proteus 66
67 MUFOLD−MD 31.89 29.51 38.45 -12.20 -8.09 -8.85 46.17 39.54 49.00 -10.16 -8.46 -6.77 MUFOLD−MD 67
68 RANDOM 18.97 16.24 18.97 -16.27 -11.31 -14.08 18.97 16.24 18.97 -20.57 -16.06 -15.08 RANDOM 68
69 OLGAFS 17.86 14.80 12.64 -16.62 -11.66 -15.78 17.86 14.80 12.64 -21.00 -16.53 -16.83 OLGAFS 69
70 BHAGEERATH                   -16.27 -11.31 -14.08                   -20.57 -16.06 -15.08 BHAGEERATH 70
71 YASARA                   -16.27 -11.31 -14.08                   -20.57 -16.06 -15.08 YASARA 71
72 mahmood−torda−server                   -16.27 -11.31 -14.08                   -20.57 -16.06 -15.08 mahmood−torda−server 72
73 schenk−torda−server                   -16.27 -11.31 -14.08                   -20.57 -16.06 -15.08 schenk−torda−server 73
74 test_http_server_01                   -16.27 -11.31 -14.08                   -20.57 -16.06 -15.08 test_http_server_01 74