T0502

X-ray Targets
387 388 389 390
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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