T0463

X-ray Targets
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T0463

putative epimerase Q89Z24_BACTN from Bacteroides thetaiotaomicron

Target type: Server only

Target sequence:

>T0463 Q89Z24_BACTN, Bacteroides thetaiotaomicron, 219 residues
MEKVKKIVLIGASGFVGSALLNEALNRGFEVTAVVRHPEKIKIENEHLKVKKADVSSLDEVCEVCKGADAVISAFNPGWNNPDIYDETIKVYLTIIDGVKKAGVNRFLMVGGAGSLFIAPGLRLMDSGEVPENILPGVKALGEFYLNFLMKEKEIDWVFFSPAADMRPGVRTGRYRLGKDDMIVDIVGNSHISVEDYAAAMIDELEHPKHHQERFTIGY

Structure:
Method: X-ray, res=2.0Å, R/Rfree=0.23/0.24
Determined by: NESG
PDB ID: 3dhn

3dhn cartoon
Cartoon diagram of 463: 3dhn

PyMOL of 3dhn

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

NAD(P)-binding Rossmann fold.

CASP category:

Comparative modeling:medium.

Closest templates:

1sb8, 1r6d, 2hun, 2pk3, 1oc2.

Target sequence - PDB file inconsistencies:

T0463    3dhn.pdb    T0463.pdb    PyMOL    PyMOL of domains    

T0463    1 MEKVKKIVLIGASGFVGSALLNEALNRGFEVTAVVRHPEKIKIENEHLKVKKADVSSLDEVCEVCKGADAVISAFNPGWNNPDIYDETIKVYLTIIDGVKKAGVNRFLMVGGAGSLFIAPGLRLMDSGEVPENILPGVKALGEFYLNFLMKEKEIDWVFFSPAADMRPGVRTGRYRLGKDDMIVDIVGNSHISVEDYAAAMIDELEHPKHHQERFTIGY----- 219
           ~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~
3dhnA    3 --KVKKIVLIGASGFVGSALLNEALNRGFEVTAVVRHPEKIKIENEHLKVKKADVSSLDEVCEVCKGADAVISAFNP------IYDETIKVYLTIIDGVKKAGVNRFLMVGGAGSLFIAPGLRLMDSGEVPENILPGVKALGEFYLNFLMKEKEIDWVFFSPAADMRPGVRTGRYRLGKDDMIVDIVGNSHISVEDYAAAMIDELEHPKHHQERFTIGYLEHHH 224

Residue change log: change 109, 125, 150, 166, 182, 201, MSE to MET; remove 220-LEHHH-224 as it is not present in target sequence;

Single domain protein: target 3-77, 84-219 ; pdb 3-77, 84-219

Sequence classification:

NAD dependent epimerase/dehydratase family PF01370 in Pfam.

Server predictions:

T0463:pdb 3-219:seq 3-219:CM_medium;   alignment

distribution of first scores
First models for T0463: 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 #
T0463 T0463 T0463 T0463
First score First Z-score Best score Best Z-score
1 ACOMPMOD 73.93 65.72 71.94 3.33 2.82 2.23 73.93 65.72 71.94 2.19 2.18 1.70 ACOMPMOD 1
2 FUGUE_KM 70.38 63.59 67.76 2.49 2.33 1.47 70.38 63.59 67.76 1.51 1.71 0.92 FUGUE_KM 2
3 FALCON 70.26 60.86 71.10 2.46 1.70 2.08 70.26 60.86 71.10 1.49 1.12 1.54 FALCON 3
4 LEE−SERVER 68.72 62.72 68.85 2.10 2.13 1.67 69.19 63.98 70.22 1.29 1.80 1.38 LEE−SERVER 4
5 LOOPP_Server 67.30 57.66 67.10 1.77 0.96 1.35 67.30 57.66 67.10 0.93 0.43 0.79 LOOPP_Server 5
6 MUSTER 66.94 59.99 68.96 1.68 1.50 1.69 66.94 59.99 68.96 0.86 0.93 1.14 MUSTER 6
7 fais−server 66.35 57.03 67.36 1.54 0.81 1.39 66.35 57.03 67.36 0.75 0.29 0.84 fais−server 7
8 Zhang−Server 65.76 60.55 65.84 1.40 1.63 1.12 70.62 61.37 70.84 1.56 1.23 1.49 Zhang−Server 8
9 YASARA 64.34 55.96 64.61 1.07 0.57 0.89 65.88 58.85 66.82 0.66 0.69 0.74 YASARA 9
10 Phyre_de_novo 63.15 54.34 65.37 0.79 0.19 1.03 63.15 54.46 65.37 0.14 -0.27 0.47 Phyre_de_novo 10
11 FEIG 62.68 53.20 62.99 0.68 -0.07 0.59 72.39 65.20 70.88 1.89 2.06 1.50 FEIG 11
12 BAKER−ROBETTA 62.56 55.21 61.85 0.65 0.39 0.39 62.68 55.88 61.85 0.05 0.04 -0.19 BAKER−ROBETTA 12
13 mGenTHREADER 62.20 53.75 58.60 0.56 0.06 -0.21 62.20 53.75 58.60 -0.04 -0.42 -0.80 mGenTHREADER 13
14 pro−sp3−TASSER 61.97 57.07 62.27 0.51 0.82 0.46 68.13 62.20 67.31 1.09 1.41 0.83 pro−sp3−TASSER 14
15 MULTICOM−REFINE 61.73 58.73 63.55 0.45 1.21 0.70 61.73 58.73 64.06 -0.13 0.66 0.23 MULTICOM−REFINE 15
16 COMA−M 61.73 56.91 61.00 0.45 0.79 0.23 62.44 57.07 61.17 0.01 0.30 -0.32 COMA−M 16
17 COMA 61.73 56.28 60.59 0.45 0.64 0.16 61.73 56.28 61.17 -0.13 0.13 -0.32 COMA 17
18 MUProt 61.37 55.69 63.75 0.37 0.50 0.73 61.37 58.14 64.07 -0.19 0.53 0.23 MUProt 18
19 RAPTOR 61.26 56.67 61.85 0.34 0.73 0.39 69.08 59.83 70.14 1.27 0.90 1.36 RAPTOR 19
20 MULTICOM−CMFR 61.14 57.58 63.18 0.31 0.94 0.63 61.37 57.58 63.54 -0.19 0.41 0.13 MULTICOM−CMFR 20
21 Pcons_multi 61.02 55.41 60.18 0.29 0.44 0.08 62.68 57.62 63.73 0.05 0.42 0.16 Pcons_multi 21
22 MULTICOM−CLUSTER 60.90 54.34 63.10 0.26 0.19 0.61 61.49 55.13 63.72 -0.17 -0.12 0.16 MULTICOM−CLUSTER 22
23 METATASSER 60.78 53.12 63.26 0.23 -0.09 0.64 63.03 59.72 63.26 0.12 0.87 0.08 METATASSER 23
24 keasar−server 60.55 53.59 61.62 0.18 0.02 0.34 67.54 60.19 68.06 0.97 0.98 0.97 keasar−server 24
25 FFASsuboptimal 60.43 55.53 60.07 0.15 0.47 0.06 60.55 55.53 60.11 -0.35 -0.03 -0.51 FFASsuboptimal 25
26 Pcons_local 60.31 54.46 59.46 0.12 0.22 -0.05 72.51 64.77 72.19 1.92 1.97 1.75 Pcons_local 26
27 Pcons_dot_net 60.31 54.46 59.46 0.12 0.22 -0.05 62.56 55.21 61.85 0.03 -0.10 -0.19 Pcons_dot_net 27
28 3DShot2 60.19 56.24 58.17 0.09 0.63 -0.29 60.19 56.24 58.17 -0.42 0.12 -0.88 3DShot2 28
29 SAM−T06−server 60.07 54.78 60.09 0.06 0.29 0.06 60.07 54.78 60.09 -0.44 -0.20 -0.52 SAM−T06−server 29
30 CpHModels 60.07 52.80 60.96 0.06 -0.16 0.22 60.07 52.80 60.96 -0.44 -0.63 -0.35 CpHModels 30
31 nFOLD3 59.95 54.19 58.94 0.03 0.16 -0.15 68.84 60.23 68.73 1.22 0.99 1.10 nFOLD3 31
32 forecast 59.72 52.21 59.62 -0.02 -0.30 -0.02 59.72 52.37 60.78 -0.51 -0.72 -0.39 forecast 32
33 GS−KudlatyPred 59.60 53.99 61.23 -0.05 0.11 0.27 65.17 55.21 64.89 0.53 -0.10 0.38 GS−KudlatyPred 33
34 HHpred5 59.36 55.09 62.75 -0.11 0.36 0.55 59.36 55.09 62.75 -0.58 -0.13 -0.02 HHpred5 34
35 FFASflextemplate 59.36 55.02 58.27 -0.11 0.35 -0.27 59.95 55.02 59.35 -0.46 -0.14 -0.66 FFASflextemplate 35
36 MULTICOM−RANK 59.12 52.09 61.15 -0.16 -0.33 0.26 60.07 52.09 61.50 -0.44 -0.78 -0.25 MULTICOM−RANK 36
37 FFASstandard 59.01 53.32 59.73 -0.19 -0.04 -0.00 65.64 56.75 65.49 0.61 0.23 0.49 FFASstandard 37
38 SAM−T02−server 58.65 53.75 57.47 -0.27 0.06 -0.42 59.60 53.75 57.95 -0.53 -0.42 -0.92 SAM−T02−server 38
39 Pushchino 58.53 53.28 53.10 -0.30 -0.05 -1.22 58.53 53.28 53.10 -0.73 -0.52 -1.83 Pushchino 39
40 SAM−T08−server 58.41 50.83 61.97 -0.33 -0.62 0.41 58.41 50.83 61.97 -0.76 -1.05 -0.17 SAM−T08−server 40
41 Frankenstein 58.06 50.99 58.91 -0.41 -0.58 -0.15 58.06 54.23 61.48 -0.82 -0.32 -0.26 Frankenstein 41
42 BioSerf 57.94 50.00 59.47 -0.44 -0.81 -0.05 57.94 50.00 59.47 -0.84 -1.23 -0.63 BioSerf 42
43 FAMSD 57.82 51.78 56.55 -0.47 -0.40 -0.58 69.91 61.22 69.65 1.42 1.20 1.27 FAMSD 43
44 HHpred2 57.58 51.03 60.81 -0.53 -0.57 0.20 57.58 51.03 60.81 -0.91 -1.01 -0.38 HHpred2 44
45 PS2−server 56.87 51.94 58.80 -0.69 -0.36 -0.17 57.23 51.94 59.10 -0.98 -0.81 -0.70 PS2−server 45
46 pipe_int 56.75 51.22 53.65 -0.72 -0.53 -1.11 56.75 51.22 53.65 -1.07 -0.97 -1.72 pipe_int 46
47 Fiser−M4T 56.63 51.98 52.74 -0.75 -0.35 -1.28 56.63 51.98 52.74 -1.09 -0.80 -1.89 Fiser−M4T 47
48 circle 56.63 49.29 60.17 -0.75 -0.97 0.08 61.26 55.02 61.42 -0.22 -0.14 -0.27 circle 48
49 Poing 56.28 52.80 54.48 -0.83 -0.16 -0.96 65.88 57.31 66.14 0.66 0.35 0.62 Poing 49
50 Phyre2 56.28 52.80 54.48 -0.83 -0.16 -0.96 65.88 57.23 66.16 0.66 0.33 0.62 Phyre2 50
51 Phragment 56.28 52.80 54.48 -0.83 -0.16 -0.96 65.17 54.46 65.70 0.53 -0.27 0.53 Phragment 51
52 FALCON_CONSENSUS 55.92 46.68 58.50 -0.92 -1.58 -0.23 70.26 60.86 71.10 1.49 1.12 1.54 FALCON_CONSENSUS 52
53 3D−JIGSAW_AEP 55.81 48.46 55.09 -0.94 -1.17 -0.85 55.81 50.04 55.96 -1.25 -1.22 -1.29 3D−JIGSAW_AEP 53
54 PSI 55.21 45.73 55.07 -1.08 -1.80 -0.85 56.63 51.94 58.91 -1.09 -0.81 -0.74 PSI 54
55 HHpred4 55.09 47.59 60.97 -1.11 -1.37 0.22 55.09 47.59 60.97 -1.38 -1.76 -0.35 HHpred4 55
56 3D−JIGSAW_V3 54.62 49.33 50.77 -1.22 -0.97 -1.64 54.62 49.68 51.14 -1.47 -1.30 -2.19 3D−JIGSAW_V3 56
57 panther_server 54.50 49.76 49.21 -1.25 -0.87 -1.93 55.69 49.76 51.84 -1.27 -1.29 -2.06 panther_server 57
58 MUFOLD−Server 52.96 44.59 53.27 -1.61 -2.06 -1.18 54.03 46.64 54.58 -1.59 -1.96 -1.55 MUFOLD−Server 58
59 3Dpro 52.84 48.18 53.22 -1.64 -1.23 -1.19 52.84 48.18 53.22 -1.81 -1.63 -1.80 3Dpro 59
60 rehtnap 46.68 37.91 36.21 -3.10 -3.60 -4.30 49.41 42.93 38.54 -2.46 -2.77 -4.55 rehtnap 60
61 FOLDpro 29.74 23.34 26.63 -7.09 -6.97 -6.06 36.26 31.91 30.75 -4.95 -5.16 -6.01 FOLDpro 61
62 Distill 29.50 25.00 34.54 -7.15 -6.59 -4.61 29.86 25.00 34.98 -6.17 -6.66 -5.22 Distill 62
63 mariner1 27.73 22.43 28.91 -7.56 -7.18 -5.64 68.01 58.85 67.59 1.06 0.69 0.89 mariner1 63
64 MUFOLD−MD 23.82 17.42 36.97 -8.49 -8.34 -4.17 25.36 20.46 36.97 -7.02 -7.64 -4.84 MUFOLD−MD 64
65 RBO−Proteus 17.54 16.94 35.04 -9.97 -8.45 -4.52 19.31 17.50 35.93 -8.17 -8.28 -5.04 RBO−Proteus 65
66 OLGAFS 14.34 11.81 0.95 -10.72 -9.63 -10.75 31.40 26.42 27.86 -5.87 -6.35 -6.55 OLGAFS 66
67 RANDOM 11.85 10.33 11.85 -11.31 -9.97 -8.76 11.85 10.33 11.85 -9.58 -9.84 -9.55 RANDOM 67
68 schenk−torda−server 10.78 9.40 15.97 -11.56 -10.19 -8.01 11.61 9.99 15.97 -9.63 -9.91 -8.78 schenk−torda−server 68
69 BHAGEERATH                   -11.31 -9.97 -8.76                   -9.58 -9.84 -9.55 BHAGEERATH 69
70 GS−MetaServer2                   -11.31 -9.97 -8.76                   -9.58 -9.84 -9.55 GS−MetaServer2 70
71 GeneSilicoMetaServer                   -11.31 -9.97 -8.76                   -9.58 -9.84 -9.55 GeneSilicoMetaServer 71
72 huber−torda−server                   -11.31 -9.97 -8.76                   -9.58 -9.84 -9.55 huber−torda−server 72
73 mahmood−torda−server                   -11.31 -9.97 -8.76                   -9.81 -10.12 -9.55 mahmood−torda−server 73
74 test_http_server_01                   -11.31 -9.97 -8.76                   -9.58 -9.84 -9.55 test_http_server_01 74