T0475

NMR Targets
437 460 462 464
466 467 468 469
471 472 473 474
475 476 480 482
484 492 498 499
500

T0475

protein Atu0742 from Agrobacterium tumefaciens

Target type: Server only

Target sequence:

>T0475 AtT8, unknown, 122 residues
LNSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERFKEPDLYGELLTRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEVENGRIAKAWFKIGEPRIVSQK

Structure:
Method: NMR
Determined by: NESG
PDB ID: 2k54

jumping through 475 NMR models
Jumping through 20 NMR models of 2k54

all 20 475 NMR models
All 20 superimposed NMR models of 2k54

PyMOL of 2k54

Domains:  PyMOL of domains

Single domain protein. Good NMR structure, only the last residue poorly ordered, but it is absent in the target sequence and was removed anyway.

Structure classification:

Cystatin-like fold, similar to Nuclear transport factor 2 (NTF2-like) proteins.

2k54_1:1-122 cartoon
Cartoon diagram of T0475: 2k54 model 1 residues 1-122

CASP category:

Comparative modeling: medium. Similar to the templates. Differences are in loops and around the C-terminus, which has a helical turn in templates, but is extended in the target NMR structure.

Closest templates:

Ketosteroid isomerase, e.g. 1isk.

Target sequence - PDB file inconsistencies:

The first residue is Leu in the target, but Met in PDB. The last PDB residue Ser123 is not in the target sequence, but it is not ordered in NMR models anyway.

T0475    2k54.pdb    T0475.pdb    PyMOL    PyMOL of domains    

T0475    1 LNSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERFKEPDLYGELLTRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEVENGRIAKAWFKIGEPRIVSQK- 122
           :|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~
2k54A    1 MNSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERFKEPDLYGELLTRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEVENGRIAKAWFKIGEPRIVSQKS 123

Residue change log: change 1 M to L; remove 123 S as it is not present in target sequence;

Single domain protein: target 1-122 ; pdb 1-122

Sequence classification:

SnoaL-like polyketide cyclase family (SnoaL) in Pfam.

Comments:

Server predictions:

T0475:pdb 1-122:seq 1-122:CM_medium;   alignment

distribution of first scores
First models for T0475: 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 #
T0475 T0475 T0475 T0475
First score First Z-score Best score Best Z-score
1 HHpred5 81.76 72.34 80.18 1.76 1.28 1.16 81.76 72.34 80.18 1.75 0.92 1.27 HHpred5 1
2 MULTICOM−CMFR 80.94 77.12 78.42 1.60 2.07 0.91 80.94 77.12 78.42 1.55 1.95 0.87 MULTICOM−CMFR 2
3 MUProt 80.94 75.75 76.74 1.60 1.85 0.68 81.76 76.43 77.58 1.75 1.80 0.68 MUProt 3
4 MULTICOM−REFINE 80.94 71.24 78.14 1.60 1.10 0.88 83.20 76.91 78.86 2.12 1.91 0.97 MULTICOM−REFINE 4
5 Phyre_de_novo 79.71 75.75 79.52 1.38 1.85 1.07 79.71 75.75 79.52 1.24 1.66 1.12 Phyre_de_novo 5
6 LEE−SERVER 79.71 74.80 77.96 1.38 1.69 0.85 80.94 76.03 78.39 1.55 1.72 0.86 LEE−SERVER 6
7 Zhang−Server 79.51 75.96 81.19 1.34 1.88 1.30 79.51 75.96 81.19 1.19 1.70 1.49 Zhang−Server 7
8 METATASSER 78.89 67.28 77.21 1.23 0.44 0.75 79.30 74.93 79.22 1.14 1.48 1.05 METATASSER 8
9 GS−KudlatyPred 78.69 73.50 76.69 1.19 1.47 0.67 78.69 73.50 76.69 0.98 1.17 0.48 GS−KudlatyPred 9
10 COMA−M 78.28 68.99 77.00 1.11 0.72 0.72 79.92 75.00 77.84 1.29 1.49 0.74 COMA−M 10
11 GeneSilicoMetaServer 77.66 70.97 75.72 1.00 1.05 0.54 77.66 70.97 75.72 0.73 0.62 0.26 GeneSilicoMetaServer 11
12 PS2−server 77.25 72.61 74.89 0.92 1.32 0.42 77.25 72.61 74.89 0.62 0.98 0.07 PS2−server 12
13 pro−sp3−TASSER 76.23 65.16 80.00 0.74 0.09 1.13 79.30 74.93 80.38 1.14 1.48 1.31 pro−sp3−TASSER 13
14 FFASstandard 75.82 65.03 72.09 0.66 0.06 0.03 76.43 69.54 75.70 0.42 0.32 0.25 FFASstandard 14
15 FFASsuboptimal 75.82 60.52 72.16 0.66 -0.68 0.04 76.03 69.94 72.26 0.32 0.40 -0.53 FFASsuboptimal 15
16 LOOPP_Server 75.41 72.68 71.50 0.59 1.34 -0.05 77.25 72.68 74.16 0.62 0.99 -0.10 LOOPP_Server 16
17 3DShot2 75.41 66.12 73.98 0.59 0.25 0.30 75.41 66.12 73.98 0.16 -0.42 -0.14 3DShot2 17
18 Frankenstein 75.41 62.43 70.11 0.59 -0.37 -0.24 75.41 63.93 76.00 0.16 -0.89 0.32 Frankenstein 18
19 MUSTER 75.20 70.56 73.83 0.55 0.98 0.28 79.71 73.57 77.63 1.24 1.19 0.69 MUSTER 19
20 circle 74.80 66.60 72.40 0.47 0.33 0.08 75.61 66.60 72.72 0.21 -0.32 -0.42 circle 20
21 fais−server 73.97 67.69 78.73 0.32 0.51 0.96 73.97 67.69 78.73 -0.20 -0.08 0.94 fais−server 21
22 Pcons_dot_net 73.77 63.32 69.19 0.28 -0.22 -0.37 77.05 67.01 72.88 0.57 -0.23 -0.39 Pcons_dot_net 22
23 Pcons_multi 73.77 63.32 69.19 0.28 -0.22 -0.37 77.46 70.36 75.24 0.68 0.49 0.15 Pcons_multi 23
24 MULTICOM−CLUSTER 73.36 69.13 67.32 0.21 0.75 -0.63 77.66 72.20 74.58 0.73 0.89 -0.00 MULTICOM−CLUSTER 24
25 3D−JIGSAW_AEP 73.16 65.64 77.66 0.17 0.17 0.81 73.16 65.64 77.66 -0.40 -0.53 0.70 3D−JIGSAW_AEP 25
26 SAM−T08−server 73.16 63.66 75.44 0.17 -0.16 0.50 73.97 67.01 75.44 -0.20 -0.23 0.19 SAM−T08−server 26
27 panther_server 72.95 66.67 77.10 0.13 0.34 0.73 72.95 66.67 77.10 -0.46 -0.30 0.57 panther_server 27
28 RAPTOR 72.75 66.19 73.80 0.10 0.26 0.27 73.16 67.69 75.27 -0.40 -0.08 0.15 RAPTOR 28
29 MUFOLD−Server 72.54 65.85 75.91 0.06 0.20 0.56 72.75 66.39 75.93 -0.51 -0.36 0.30 MUFOLD−Server 29
30 BioSerf 72.34 64.14 75.30 0.02 -0.08 0.48 72.34 64.14 75.30 -0.61 -0.85 0.16 BioSerf 30
31 keasar−server 72.13 64.89 71.44 -0.02 0.04 -0.06 75.20 67.83 72.37 0.11 -0.05 -0.50 keasar−server 31
32 PSI 72.13 63.93 78.03 -0.02 -0.12 0.86 77.66 71.24 78.03 0.73 0.68 0.78 PSI 32
33 pipe_int 71.93 66.19 75.90 -0.06 0.26 0.56 75.61 68.58 75.90 0.21 0.11 0.30 pipe_int 33
34 3D−JIGSAW_V3 71.93 61.95 78.31 -0.06 -0.45 0.90 71.93 64.48 78.32 -0.71 -0.78 0.84 3D−JIGSAW_V3 34
35 GS−MetaServer2 71.72 65.03 73.11 -0.09 0.06 0.17 76.03 69.19 75.47 0.32 0.24 0.20 GS−MetaServer2 35
36 mGenTHREADER 71.72 62.98 75.57 -0.09 -0.28 0.52 71.72 62.98 75.57 -0.77 -1.10 0.22 mGenTHREADER 36
37 FALCON 71.31 62.43 73.40 -0.17 -0.37 0.22 71.31 62.43 73.40 -0.87 -1.22 -0.27 FALCON 37
38 SAM−T06−server 71.11 65.78 75.39 -0.21 0.19 0.49 75.82 70.63 75.39 0.26 0.55 0.18 SAM−T06−server 38
39 HHpred2 71.11 63.73 77.92 -0.21 -0.15 0.85 71.11 63.73 77.92 -0.92 -0.94 0.75 HHpred2 39
40 FFASflextemplate 71.11 60.72 69.29 -0.21 -0.65 -0.36 71.72 62.84 70.13 -0.77 -1.13 -1.01 FFASflextemplate 40
41 MULTICOM−RANK 70.90 65.98 76.35 -0.25 0.22 0.63 73.36 69.13 76.44 -0.35 0.23 0.42 MULTICOM−RANK 41
42 nFOLD3 70.90 65.85 71.46 -0.25 0.20 -0.06 71.11 65.85 71.85 -0.92 -0.48 -0.62 nFOLD3 42
43 FUGUE_KM 70.90 62.30 70.17 -0.25 -0.39 -0.24 71.31 62.30 70.17 -0.87 -1.25 -1.00 FUGUE_KM 43
44 COMA 70.70 64.55 68.37 -0.28 -0.02 -0.49 70.70 66.87 77.84 -1.02 -0.26 0.74 COMA 44
45 forecast 70.70 63.87 67.99 -0.28 -0.13 -0.54 76.43 67.83 73.38 0.42 -0.05 -0.27 forecast 45
46 BAKER−ROBETTA 70.29 63.18 69.65 -0.36 -0.24 -0.31 73.36 66.87 72.61 -0.35 -0.26 -0.45 BAKER−ROBETTA 46
47 rehtnap 70.29 59.49 65.51 -0.36 -0.86 -0.88 70.29 59.49 65.51 -1.12 -1.85 -2.05 rehtnap 47
48 Distill 70.08 64.34 64.77 -0.40 -0.05 -0.99 70.90 66.46 65.61 -0.97 -0.35 -2.03 Distill 48
49 FEIG 69.67 60.52 72.85 -0.47 -0.68 0.14 78.48 72.88 77.60 0.93 1.04 0.68 FEIG 49
50 FAMSD 69.47 63.32 63.16 -0.51 -0.22 -1.21 74.80 69.81 72.82 0.01 0.37 -0.40 FAMSD 50
51 Poing 68.85 60.52 73.43 -0.62 -0.68 0.22 73.77 66.53 77.87 -0.25 -0.33 0.74 Poing 51
52 Phyre2 68.85 60.52 73.43 -0.62 -0.68 0.22 73.77 66.53 77.87 -0.25 -0.33 0.74 Phyre2 52
53 Phragment 68.85 60.52 73.43 -0.62 -0.68 0.22 73.77 66.53 77.87 -0.25 -0.33 0.74 Phragment 53
54 SAM−T02−server 68.65 60.18 65.16 -0.66 -0.74 -0.93 73.36 65.57 71.72 -0.35 -0.54 -0.65 SAM−T02−server 54
55 Pcons_local 68.44 63.66 68.46 -0.70 -0.16 -0.47 73.57 67.01 71.23 -0.30 -0.23 -0.76 Pcons_local 55
56 HHpred4 68.24 60.59 74.89 -0.74 -0.67 0.42 68.24 60.59 74.89 -1.64 -1.61 0.07 HHpred4 56
57 ACOMPMOD 67.01 57.85 70.74 -0.96 -1.13 -0.16 77.46 67.62 73.43 0.68 -0.10 -0.26 ACOMPMOD 57
58 mariner1 65.57 57.38 57.60 -1.23 -1.21 -1.99 77.25 68.24 73.72 0.62 0.04 -0.20 mariner1 58
59 CpHModels 65.37 59.63 65.22 -1.26 -0.83 -0.92 65.37 59.63 65.22 -2.36 -1.82 -2.12 CpHModels 59
60 huber−torda−server 63.32 61.13 55.34 -1.64 -0.58 -2.30 63.32 61.13 55.34 -2.87 -1.50 -4.35 huber−torda−server 60
61 Pushchino 54.71 44.47 45.29 -3.23 -3.35 -3.70 54.71 44.47 45.29 -5.04 -5.09 -6.63 Pushchino 61
62 FOLDpro 49.80 41.73 43.44 -4.13 -3.81 -3.96 63.93 56.83 62.55 -2.72 -2.43 -2.72 FOLDpro 62
63 Fiser−M4T 38.32 37.09 21.71 -6.25 -4.58 -6.99 38.32 37.09 21.71 -9.15 -6.68 -11.96 Fiser−M4T 63
64 RBO−Proteus 34.84 29.64 41.88 -6.89 -5.82 -4.18 34.84 29.64 43.93 -10.02 -8.29 -6.93 RBO−Proteus 64
65 MUFOLD−MD 29.10 22.95 41.02 -7.95 -6.93 -4.30 30.94 26.43 46.87 -11.00 -8.98 -6.27 MUFOLD−MD 65
66 FALCON_CONSENSUS 26.23 22.54 38.93 -8.48 -7.00 -4.59 71.31 62.43 73.40 -0.87 -1.22 -0.27 FALCON_CONSENSUS 66
67 OLGAFS 17.42 14.69 12.19 -10.10 -8.30 -8.32 27.46 24.59 20.31 -11.88 -9.38 -12.28 OLGAFS 67
68 schenk−torda−server 15.98 14.21 18.96 -10.37 -8.38 -7.37 17.21 14.41 21.26 -14.45 -11.58 -12.06 schenk−torda−server 68
69 RANDOM 15.83 13.24 15.83 -10.39 -8.54 -7.81 15.83 13.24 15.83 -14.80 -11.83 -13.29 RANDOM 69
70 mahmood−torda−server 13.93 10.66 17.94 -10.74 -8.97 -7.51 17.01 14.34 23.52 -14.50 -11.59 -11.55 mahmood−torda−server 70
71 3Dpro                   -10.39 -8.54 -7.81                   -14.80 -11.83 -13.29 3Dpro 71
72 BHAGEERATH                   -10.39 -8.54 -7.81                   -14.80 -11.83 -13.29 BHAGEERATH 72
73 YASARA                   -10.39 -8.54 -7.81                   -14.80 -11.83 -13.29 YASARA 73
74 test_http_server_01                   -10.39 -8.54 -7.81                   -14.80 -11.83 -13.29 test_http_server_01 74