T0503

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

T0503

cyclic nucleotide binding regulatory protein Cytophaga hutchinsonii

Target type: Server only

Target sequence:

>T0503 Cyclic nucleotide binding regulatory protein, Cytophaga hutchinsonii, 191 residues
MHTALINHIRKFIFLTDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKGIEQTTQFAIENWWLSDYMAFQKQQPADFYIQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAAAQLRSKFQHMYSKEEQYHNFSSRFPEFIQRVPQYLLASYLGFTPEYLSEIRKKYIS

Structure:
Method: X-ray, res=1.8Å, R/Rfree=0.17/0.19
Determined by: MCSG
PDB ID: 3dn7

3dn7_A cartoon
Cartoon diagram of 503: 3dn7 chain A

PyMOL of 3dn7

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Double-stranded β-helix fold.

CASP category:

Comparative modeling:medium.

Closest templates:

1zyb, 1hw5, 2gau, 2oz6, 2bgc.

Target sequence - PDB file inconsistencies:

T0503    3dn7.pdb    T0503.pdb    PyMOL    PyMOL of domains    

T0503    1 MHTALINHIRKFIFLTDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKGIEQTTQFAIENWWLSDYMAFQKQQPADFYIQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAAAQLRSKFQHMYSKEEQYHNFSSRFPEFIQRVPQYLLASYLGFTPEYLSEIRKKYIS 191
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3dn7A    1 MHTALINHIRKFIFLTDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKGIEQTTQFAIENWWLSDYMAFQKQQPADFYIQSVENCELLSITYTEQENLFERIPALERYFRLVYQKSFAAAQLRSKFQHMY--------------------------------------------- 146

Residue change log: change 1, 83, 145, MSE to MET;

Single domain protein: target 1-146 ; pdb 1-146

Sequence classification:

Cyclic nucleotide-binding domain (cNMP_binding) in Pfam.

Comments:

This protein is a homolog of T0414.

Server predictions:

T0503:pdb 1-146:seq 1-146:CM_medium;   alignment

distribution of first scores
First models for T0503: 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 #
T0503 T0503 T0503 T0503
First score First Z-score Best score Best Z-score
1 METATASSER 73.12 58.16 78.98 2.41 1.92 1.27 73.12 60.96 78.98 2.79 2.76 0.98 METATASSER 1
2 pro−sp3−TASSER 71.58 58.90 76.32 1.96 2.13 0.60 71.58 58.90 79.51 2.16 1.99 1.13 pro−sp3−TASSER 2
3 Zhang−Server 71.06 60.10 79.18 1.81 2.46 1.32 71.06 60.10 79.90 1.94 2.44 1.24 Zhang−Server 3
4 HHpred5 71.06 55.88 79.58 1.81 1.29 1.43 71.06 55.88 79.58 1.94 0.87 1.15 HHpred5 4
5 COMA−M 69.52 56.96 78.80 1.36 1.59 1.23 69.52 56.96 78.80 1.30 1.27 0.93 COMA−M 5
6 3DShot2 69.18 52.51 72.93 1.26 0.35 -0.26 69.18 52.51 72.93 1.16 -0.38 -0.75 3DShot2 6
7 pipe_int 68.84 54.57 76.57 1.16 0.92 0.66 69.01 55.54 78.47 1.09 0.74 0.83 pipe_int 7
8 Fiser−M4T 68.49 52.97 77.44 1.05 0.48 0.88 68.49 52.97 77.44 0.88 -0.21 0.54 Fiser−M4T 8
9 BioSerf 68.32 56.91 77.98 1.00 1.57 1.02 68.32 56.91 77.98 0.81 1.25 0.69 BioSerf 9
10 MULTICOM−REFINE 68.32 55.88 76.11 1.00 1.29 0.54 68.32 55.88 76.11 0.81 0.87 0.16 MULTICOM−REFINE 10
11 MUFOLD−Server 68.32 55.19 74.00 1.00 1.10 0.01 68.32 55.19 76.00 0.81 0.61 0.13 MUFOLD−Server 11
12 fais−server 67.81 55.48 75.79 0.85 1.18 0.46 67.81 55.48 77.07 0.60 0.72 0.43 fais−server 12
13 MUProt 67.64 54.74 75.91 0.80 0.97 0.49 67.81 54.74 76.56 0.60 0.45 0.29 MUProt 13
14 MULTICOM−CLUSTER 67.47 54.22 77.05 0.76 0.83 0.78 71.23 58.28 80.36 2.01 1.76 1.38 MULTICOM−CLUSTER 14
15 RAPTOR 67.30 56.68 77.69 0.71 1.51 0.95 67.30 56.68 78.02 0.39 1.17 0.71 RAPTOR 15
16 COMA 67.30 54.85 75.93 0.71 1.00 0.50 67.30 54.85 78.80 0.39 0.49 0.93 COMA 16
17 LEE−SERVER 67.30 45.03 79.24 0.71 -1.73 1.34 67.30 52.80 79.27 0.39 -0.27 1.06 LEE−SERVER 17
18 MUSTER 66.27 54.17 75.29 0.40 0.81 0.34 69.35 55.99 79.79 1.23 0.91 1.21 MUSTER 18
19 YASARA 66.27 53.48 75.27 0.40 0.62 0.33 66.27 53.48 75.27 -0.04 -0.02 -0.08 YASARA 19
20 Frankenstein 66.10 53.65 73.23 0.35 0.67 -0.19 66.10 53.65 74.56 -0.11 0.04 -0.28 Frankenstein 20
21 FALCON 65.92 53.02 78.58 0.30 0.49 1.17 66.10 54.22 78.58 -0.11 0.25 0.87 FALCON 21
22 PSI 65.92 52.57 73.59 0.30 0.37 -0.10 65.92 52.57 73.59 -0.18 -0.36 -0.56 PSI 22
23 CpHModels 65.92 51.08 72.06 0.30 -0.05 -0.49 65.92 51.08 72.06 -0.18 -0.91 -1.00 CpHModels 23
24 3D−JIGSAW_V3 65.92 50.23 76.35 0.30 -0.28 0.60 66.10 52.85 77.28 -0.11 -0.25 0.49 3D−JIGSAW_V3 24
25 FALCON_CONSENSUS 65.75 52.97 78.31 0.25 0.48 1.10 66.10 54.22 78.58 -0.11 0.25 0.87 FALCON_CONSENSUS 25
26 GS−KudlatyPred 65.75 52.57 78.22 0.25 0.37 1.08 65.75 52.57 78.22 -0.25 -0.36 0.76 GS−KudlatyPred 26
27 HHpred2 65.75 50.69 74.39 0.25 -0.16 0.11 65.75 50.69 74.39 -0.25 -1.06 -0.33 HHpred2 27
28 keasar−server 65.75 49.37 76.77 0.25 -0.52 0.71 66.27 51.66 77.27 -0.04 -0.70 0.49 keasar−server 28
29 GS−MetaServer2 65.58 51.88 71.71 0.20 0.18 -0.58 65.58 51.88 71.71 -0.32 -0.61 -1.10 GS−MetaServer2 29
30 3D−JIGSAW_AEP 65.58 51.14 73.21 0.20 -0.03 -0.19 67.64 57.36 76.09 0.53 1.42 0.15 3D−JIGSAW_AEP 30
31 PS2−server 65.41 52.97 73.85 0.15 0.48 -0.03 67.98 54.28 80.19 0.67 0.28 1.33 PS2−server 31
32 MULTICOM−RANK 65.07 51.26 73.67 0.05 0.00 -0.08 66.27 52.17 74.28 -0.04 -0.51 -0.36 MULTICOM−RANK 32
33 GeneSilicoMetaServer 65.07 50.91 70.64 0.05 -0.09 -0.85 65.58 52.34 71.71 -0.32 -0.44 -1.10 GeneSilicoMetaServer 33
34 Pcons_local 64.73 50.80 71.63 -0.05 -0.12 -0.60 65.07 51.37 72.58 -0.54 -0.80 -0.85 Pcons_local 34
35 circle 64.56 51.14 70.81 -0.10 -0.03 -0.80 69.01 55.14 78.58 1.09 0.60 0.87 circle 35
36 MULTICOM−CMFR 64.56 50.97 75.68 -0.10 -0.08 0.43 68.49 52.57 76.51 0.88 -0.36 0.27 MULTICOM−CMFR 36
37 Poing 64.56 49.83 76.36 -0.10 -0.39 0.61 64.90 50.06 76.36 -0.61 -1.29 0.23 Poing 37
38 Phyre2 64.56 49.83 76.20 -0.10 -0.39 0.57 65.24 50.40 78.31 -0.46 -1.16 0.79 Phyre2 38
39 nFOLD3 64.38 52.17 68.40 -0.15 0.26 -1.42 67.30 53.71 78.38 0.39 0.06 0.81 nFOLD3 39
40 SAM−T08−server 64.38 51.14 80.42 -0.15 -0.03 1.64 64.56 52.23 81.98 -0.75 -0.48 1.84 SAM−T08−server 40
41 Pushchino 64.38 50.57 70.44 -0.15 -0.19 -0.90 64.38 50.57 70.44 -0.82 -1.10 -1.46 Pushchino 41
42 Phragment 64.38 49.66 75.83 -0.15 -0.44 0.47 64.73 49.77 77.12 -0.68 -1.40 0.45 Phragment 42
43 BAKER−ROBETTA 64.21 52.34 76.69 -0.20 0.30 0.69 65.75 52.97 78.22 -0.25 -0.21 0.76 BAKER−ROBETTA 43
44 SAM−T02−server 63.87 51.43 71.48 -0.30 0.05 -0.63 64.21 52.00 71.48 -0.89 -0.57 -1.17 SAM−T02−server 44
45 Phyre_de_novo 63.87 48.69 77.41 -0.30 -0.71 0.87 65.24 48.69 77.41 -0.46 -1.80 0.53 Phyre_de_novo 45
46 forecast 63.70 50.46 71.49 -0.35 -0.22 -0.63 65.58 52.80 73.99 -0.32 -0.27 -0.45 forecast 46
47 mGenTHREADER 63.70 48.40 71.19 -0.35 -0.79 -0.71 63.70 48.40 71.19 -1.10 -1.91 -1.25 mGenTHREADER 47
48 FUGUE_KM 63.53 51.08 68.26 -0.40 -0.05 -1.45 63.53 54.05 68.85 -1.17 0.19 -1.92 FUGUE_KM 48
49 Pcons_dot_net 63.53 48.34 69.26 -0.40 -0.81 -1.20 64.73 51.14 72.58 -0.68 -0.89 -0.85 Pcons_dot_net 49
50 Pcons_multi 63.53 48.34 69.26 -0.40 -0.81 -1.20 64.56 52.00 74.73 -0.75 -0.57 -0.24 Pcons_multi 50
51 ACOMPMOD 63.36 46.69 69.34 -0.45 -1.27 -1.18 65.58 60.45 70.40 -0.32 2.57 -1.47 ACOMPMOD 51
52 SAM−T06−server 62.84 48.40 80.02 -0.60 -0.79 1.54 64.04 50.57 80.02 -0.96 -1.10 1.28 SAM−T06−server 52
53 LOOPP_Server 61.13 48.80 67.08 -1.10 -0.68 -1.75 64.73 52.74 71.25 -0.68 -0.30 -1.23 LOOPP_Server 53
54 FFASstandard 59.59 49.09 66.04 -1.55 -0.60 -2.02 67.12 53.88 74.90 0.31 0.13 -0.19 FFASstandard 54
55 FFASflextemplate 58.90 41.67 66.04 -1.75 -2.66 -2.02 59.59 49.09 66.04 -2.80 -1.65 -2.72 FFASflextemplate 55
56 FFASsuboptimal 58.90 41.67 66.04 -1.75 -2.66 -2.02 58.90 41.67 66.04 -3.09 -4.40 -2.72 FFASsuboptimal 56
57 panther_server 58.73 45.49 63.64 -1.80 -1.60 -2.63 65.07 52.85 69.40 -0.54 -0.25 -1.76 panther_server 57
58 rehtnap 58.22 43.04 64.12 -1.95 -2.28 -2.51 58.22 44.46 65.04 -3.37 -3.37 -3.01 rehtnap 58
59 FOLDpro 57.02 44.18 68.22 -2.31 -1.96 -1.46 63.53 57.13 68.22 -1.17 1.33 -2.10 FOLDpro 59
60 HHpred4 56.68 41.27 70.18 -2.41 -2.77 -0.96 56.68 41.27 70.18 -4.00 -4.55 -1.54 HHpred4 60
61 FEIG 56.16 46.40 72.36 -2.56 -1.35 -0.41 66.78 53.88 73.96 0.17 0.13 -0.46 FEIG 61
62 OLGAFS 55.31 47.43 57.71 -2.81 -1.06 -4.14 55.82 47.43 58.13 -4.36 -2.27 -4.99 OLGAFS 62
63 3Dpro 54.62 47.66 67.67 -3.01 -1.00 -1.60 62.33 55.82 68.99 -1.67 0.85 -1.88 3Dpro 63
64 Distill 53.94 40.18 63.07 -3.21 -3.08 -2.77 55.99 45.38 63.26 -4.29 -3.03 -3.52 Distill 64
65 mariner1 29.11 22.60 34.03 -10.48 -7.96 -10.16 57.88 48.97 69.55 -3.51 -1.69 -1.72 mariner1 65
66 MUFOLD−MD 27.40 20.15 40.21 -10.98 -8.64 -8.59 27.40 25.23 40.81 -16.11 -10.51 -9.94 MUFOLD−MD 66
67 RBO−Proteus 25.51 20.15 35.56 -11.53 -8.64 -9.77 26.71 21.86 37.04 -16.39 -11.76 -11.02 RBO−Proteus 67
68 RANDOM 14.94 13.01 14.94 -14.63 -10.63 -15.01 14.94 13.01 14.94 -21.26 -15.04 -17.34 RANDOM 68
69 FAMSD 13.36 10.85 80.28 -15.09 -11.23 1.60 66.95 54.17 80.28 0.24 0.24 1.35 FAMSD 69
70 BHAGEERATH                   -14.63 -10.63 -15.01                   -21.26 -15.04 -17.34 BHAGEERATH 70
71 huber−torda−server                   -14.63 -10.63 -15.01                   -21.26 -15.04 -17.34 huber−torda−server 71
72 mahmood−torda−server                   -14.63 -10.63 -15.01                   -21.26 -15.04 -17.34 mahmood−torda−server 72
73 schenk−torda−server                   -14.63 -10.63 -15.01                   -21.26 -15.04 -17.34 schenk−torda−server 73
74 test_http_server_01                   -14.63 -10.63 -15.01                   -21.26 -15.04 -17.34 test_http_server_01 74