T0509

Targets
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411 412 413 414
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419 420 421 422
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T0509

methyltransferase Q8NRD3_CORGL from Corynebacterium glutamicum

Target type: Server only

Target sequence:

>T0509 Q8NRD3_CORGL , Corynebacterium glutamicum, 213 residues
MSNAFEYLRTYVESTTETDAAVARAREDAAEFGLPAPDEMTGQLLTTLAATTNGNGSTGAIAITPAAGLVGLYILNGLADNTTLTCIDPESEHQRQAKALFREAGYSPSRVRFLLSRPLDVMSRLANDSYQLVFGQVSPMDLKALVDAAWPLLRRGGALVLADALLDGTIADQTRKDRDTQAARDADEYIRSIEGAHVARLPLGAGLTVVTKA

Structure:
Method: X-ray, res=2.25Å, R/Rfree=0.21/0.23
Determined by: NESG
PDB ID: 3dr5

3dr5 cartoon
Cartoon diagram of 509: 3dr5

PyMOL of 3dr5

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

SAM-dependent methyltransferase fold.

CASP category:

Comparative modeling:medium.

Closest templates:

3cbg, 2avd, 2hnk, 3c3y, 3c3p.

Target sequence - PDB file inconsistencies:

T0509    3dr5.pdb    T0509.pdb    PyMOL    PyMOL of domains    

T0509    1 MSNAFEYLRTYVESTTETDAAVARAREDAAEFGLPAPDEMTGQLLTTLAATTNGNGSTGAIAITPAAGLVGLYILNGLADNTTLTCIDPESEHQRQAKALFREAGYSPSRVRFLLSRPLDVMSRLANDSYQLVFGQVSPMDLKALVDAAWPLLRRGGALVLADALLDGTIADQTRKDRDTQAARDADEYIRSIEGAHVARLPLGAGLTVVTKA----- 213
           ~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~
3dr5A    3 --NAFEYLRTYVESTTETDAAVARAREDAAEFGLPAPDEMTGQLLTTLAATTNGNGSTGAIAITPAAGLVGLYILNGLADNTTLTCIDPESEHQRQAKALFREAGYSPSRVRFLLSRPLDVMSRLANDSYQLVFGQVSPMDLKALVDAAWPLLRRGGALVLADALLDGTIADQTRKDRDTQAARDADEYIRSIEGAHVARLPLGAGLTVVTKALEHHH 218

Residue change log: change 40, 122, 140, MSE to MET; remove 214-LEHHH-218 as it is not present in target sequence;

Single domain protein: target 3-213 ; pdb 3-213

Sequence classification:

O-methyltransferase family (Methyltransf_3) in Pfam.

Server predictions:

T0509:pdb 3-213:seq 3-213:CM_medium;   alignment

distribution of first scores
First models for T0509: 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 #
T0509 T0509 T0509 T0509
First score First Z-score Best score Best Z-score
1 MULTICOM−RANK 78.08 71.92 79.02 1.26 1.19 1.28 78.08 71.92 79.02 1.23 1.05 1.24 MULTICOM−RANK 1
2 Phyre_de_novo 77.49 72.59 77.58 1.13 1.29 1.00 77.49 72.59 77.58 1.08 1.17 0.90 Phyre_de_novo 2
3 MULTICOM−REFINE 77.49 72.59 79.01 1.13 1.29 1.28 77.49 72.59 79.01 1.08 1.17 1.24 MULTICOM−REFINE 3
4 GS−KudlatyPred 77.25 72.75 77.88 1.08 1.31 1.06 77.25 72.75 78.54 1.02 1.20 1.13 GS−KudlatyPred 4
5 HHpred5 77.01 70.93 79.97 1.03 1.05 1.47 77.01 70.93 79.97 0.95 0.87 1.47 HHpred5 5
6 MUProt 77.01 68.96 78.54 1.03 0.78 1.19 77.25 71.52 78.91 1.02 0.97 1.21 MUProt 6
7 LEE−SERVER 76.90 68.76 79.62 1.01 0.75 1.40 78.08 72.67 80.56 1.23 1.19 1.61 LEE−SERVER 7
8 Pushchino 76.66 70.18 75.95 0.96 0.95 0.68 76.66 70.18 75.95 0.86 0.73 0.51 Pushchino 8
9 Zhang−Server 76.66 67.65 77.47 0.96 0.59 0.98 77.13 72.08 78.06 0.98 1.08 1.01 Zhang−Server 9
10 PS2−server 76.54 69.59 77.14 0.94 0.87 0.91 76.54 69.59 77.14 0.83 0.62 0.79 PS2−server 10
11 MUSTER 76.30 70.38 77.79 0.89 0.98 1.04 76.30 70.38 77.79 0.77 0.76 0.95 MUSTER 11
12 MULTICOM−CMFR 76.19 68.60 77.01 0.86 0.73 0.89 76.19 70.58 77.99 0.74 0.80 1.00 MULTICOM−CMFR 12
13 3D−JIGSAW_V3 76.07 67.42 75.69 0.84 0.56 0.63 76.66 68.29 76.06 0.86 0.38 0.54 3D−JIGSAW_V3 13
14 MULTICOM−CLUSTER 75.95 66.94 76.76 0.81 0.49 0.84 76.66 71.68 77.47 0.86 1.00 0.87 MULTICOM−CLUSTER 14
15 Pcons_multi 75.83 69.19 78.19 0.79 0.81 1.12 77.13 72.23 78.98 0.98 1.10 1.23 Pcons_multi 15
16 PSI 75.59 69.27 75.77 0.74 0.82 0.64 75.59 69.27 75.77 0.58 0.56 0.47 PSI 16
17 GS−MetaServer2 75.12 69.59 76.37 0.64 0.87 0.76 75.83 69.59 76.37 0.64 0.62 0.61 GS−MetaServer2 17
18 Frankenstein 74.88 67.85 74.93 0.59 0.62 0.48 75.71 69.47 77.14 0.61 0.60 0.79 Frankenstein 18
19 FFASstandard 74.76 68.76 74.89 0.56 0.75 0.47 74.76 68.76 75.20 0.36 0.47 0.33 FFASstandard 19
20 RAPTOR 74.64 69.19 76.14 0.54 0.81 0.72 75.47 70.50 76.14 0.55 0.79 0.56 RAPTOR 20
21 Phragment 74.64 68.88 74.86 0.54 0.76 0.47 74.64 68.88 75.24 0.33 0.49 0.34 Phragment 21
22 HHpred2 74.64 68.09 74.93 0.54 0.65 0.48 74.64 68.09 74.93 0.33 0.34 0.27 HHpred2 22
23 Phyre2 74.53 68.92 74.96 0.52 0.77 0.49 74.53 68.92 75.22 0.30 0.50 0.34 Phyre2 23
24 Poing 74.41 69.04 74.98 0.49 0.79 0.49 74.41 69.04 75.25 0.27 0.52 0.35 Poing 24
25 HHpred4 74.29 67.02 75.45 0.47 0.50 0.58 74.29 67.02 75.45 0.24 0.15 0.39 HHpred4 25
26 fais−server 73.70 68.80 75.54 0.34 0.75 0.60 76.30 69.59 77.56 0.77 0.62 0.89 fais−server 26
27 FFASflextemplate 73.70 67.06 70.97 0.34 0.51 -0.30 74.17 68.88 71.75 0.21 0.49 -0.48 FFASflextemplate 27
28 nFOLD3 73.70 65.32 73.50 0.34 0.26 0.20 73.93 68.56 74.26 0.14 0.43 0.11 nFOLD3 28
29 3DShot2 73.70 62.16 70.72 0.34 -0.19 -0.35 73.70 62.16 70.72 0.08 -0.75 -0.73 3DShot2 29
30 FFASsuboptimal 73.46 62.95 73.47 0.29 -0.07 0.19 74.76 69.16 74.89 0.36 0.54 0.26 FFASsuboptimal 30
31 METATASSER 73.34 63.78 72.13 0.27 0.04 -0.07 73.34 63.78 72.68 -0.01 -0.45 -0.26 METATASSER 31
32 pipe_int 73.10 67.65 75.01 0.22 0.59 0.49 74.53 69.00 75.86 0.30 0.51 0.49 pipe_int 32
33 COMA 72.87 65.92 71.83 0.17 0.35 -0.13 72.87 65.92 71.83 -0.13 -0.06 -0.47 COMA 33
34 COMA−M 72.87 65.92 71.83 0.17 0.35 -0.13 73.70 65.92 71.83 0.08 -0.06 -0.47 COMA−M 34
35 3D−JIGSAW_AEP 72.87 64.42 72.45 0.17 0.13 -0.01 74.41 64.53 74.31 0.27 -0.31 0.12 3D−JIGSAW_AEP 35
36 FAMSD 72.39 64.34 73.86 0.07 0.12 0.27 76.54 70.77 75.84 0.83 0.84 0.49 FAMSD 36
37 pro−sp3−TASSER 72.28 62.95 73.08 0.05 -0.07 0.11 73.10 63.70 73.72 -0.07 -0.46 -0.02 pro−sp3−TASSER 37
38 FALCON 72.04 64.45 72.48 -0.00 0.14 -0.00 72.04 64.45 72.48 -0.35 -0.33 -0.31 FALCON 38
39 FUGUE_KM 72.04 64.45 71.98 -0.00 0.14 -0.10 72.04 64.45 71.98 -0.35 -0.33 -0.43 FUGUE_KM 39
40 Fiser−M4T 72.04 61.14 71.01 -0.00 -0.33 -0.29 72.04 61.14 71.01 -0.35 -0.94 -0.66 Fiser−M4T 40
41 Pcons_local 71.92 62.76 71.86 -0.03 -0.10 -0.13 74.53 68.21 76.14 0.30 0.36 0.56 Pcons_local 41
42 GeneSilicoMetaServer 71.56 64.93 69.45 -0.10 0.21 -0.60 75.83 69.51 76.24 0.64 0.60 0.58 GeneSilicoMetaServer 42
43 circle 71.33 58.69 71.31 -0.15 -0.68 -0.23 72.16 65.44 73.44 -0.32 -0.14 -0.08 circle 43
44 huber−torda−server 71.21 65.13 68.14 -0.18 0.23 -0.86 71.21 65.13 68.84 -0.57 -0.20 -1.18 huber−torda−server 44
45 3Dpro 70.62 63.43 70.62 -0.30 -0.01 -0.37 70.62 63.43 70.62 -0.73 -0.51 -0.75 3Dpro 45
46 CpHModels 70.50 59.44 71.75 -0.32 -0.57 -0.15 70.50 59.44 71.75 -0.76 -1.25 -0.48 CpHModels 46
47 BAKER−ROBETTA 70.26 53.75 71.15 -0.37 -1.38 -0.27 71.21 60.62 71.58 -0.57 -1.03 -0.53 BAKER−ROBETTA 47
48 BioSerf 70.14 64.38 71.44 -0.40 0.13 -0.21 70.14 64.38 71.44 -0.85 -0.34 -0.56 BioSerf 48
49 LOOPP_Server 68.60 54.30 70.24 -0.72 -1.30 -0.44 69.91 60.90 71.93 -0.91 -0.98 -0.44 LOOPP_Server 49
50 mGenTHREADER 68.36 56.28 65.79 -0.77 -1.02 -1.32 68.36 56.28 65.79 -1.32 -1.83 -1.90 mGenTHREADER 50
51 SAM−T08−server 68.01 54.38 72.68 -0.84 -1.29 0.04 70.85 66.90 72.68 -0.67 0.12 -0.26 SAM−T08−server 51
52 Pcons_dot_net 68.01 46.92 67.42 -0.84 -2.34 -1.00 74.53 68.21 76.14 0.30 0.36 0.56 Pcons_dot_net 52
53 ACOMPMOD 67.89 53.40 70.30 -0.87 -1.43 -0.43 67.89 53.40 70.30 -1.44 -2.36 -0.83 ACOMPMOD 53
54 FEIG 65.76 55.57 70.21 -1.31 -1.12 -0.45 75.00 70.46 75.90 0.42 0.78 0.50 FEIG 54
55 SAM−T02−server 62.20 51.78 62.30 -2.06 -1.65 -2.01 62.80 54.74 62.94 -2.78 -2.11 -2.58 SAM−T02−server 55
56 rehtnap 61.73 55.33 55.87 -2.16 -1.15 -3.28 62.68 55.33 60.73 -2.81 -2.01 -3.10 rehtnap 56
57 MUFOLD−Server 60.66 46.29 63.37 -2.38 -2.43 -1.80 60.66 48.54 63.38 -3.34 -3.25 -2.47 MUFOLD−Server 57
58 SAM−T06−server 60.07 50.04 64.24 -2.50 -1.90 -1.63 64.57 52.01 64.24 -2.32 -2.62 -2.27 SAM−T06−server 58
59 panther_server 59.83 48.30 57.36 -2.55 -2.15 -2.98 68.96 58.77 66.92 -1.16 -1.37 -1.63 panther_server 59
60 Distill 57.70 46.25 61.11 -3.00 -2.44 -2.24 60.31 50.99 61.11 -3.44 -2.80 -3.01 Distill 60
61 FALCON_CONSENSUS 54.50 45.50 53.95 -3.66 -2.54 -3.65 72.04 64.45 72.48 -0.35 -0.33 -0.31 FALCON_CONSENSUS 61
62 forecast 44.91 39.69 49.16 -5.67 -3.37 -4.60 52.13 43.68 54.87 -5.59 -4.15 -4.49 forecast 62
63 FOLDpro 38.74 32.82 35.42 -6.95 -4.34 -7.31 43.72 37.95 43.97 -7.80 -5.20 -7.08 FOLDpro 63
64 MUFOLD−MD 28.91 20.54 45.96 -9.01 -6.07 -5.23 29.15 24.09 45.96 -11.63 -7.75 -6.61 MUFOLD−MD 64
65 RBO−Proteus 26.18 20.81 45.14 -9.58 -6.04 -5.39 28.91 26.62 45.85 -11.69 -7.29 -6.63 RBO−Proteus 65
66 mariner1 18.72 12.72 19.82 -11.13 -7.18 -10.38 47.51 41.55 45.90 -6.80 -4.54 -6.62 mariner1 66
67 RANDOM 12.82 10.85 12.82 -12.36 -7.45 -11.76 12.82 10.85 12.82 -15.92 -10.19 -14.47 RANDOM 67
68 schenk−torda−server 10.31 7.31 9.71 -12.89 -7.95 -12.37 11.26 10.35 16.46 -16.33 -10.28 -13.61 schenk−torda−server 68
69 BHAGEERATH                   -12.36 -7.45 -11.76                   -15.92 -10.19 -14.47 BHAGEERATH 69
70 OLGAFS                   -12.36 -7.45 -11.76                   -15.92 -10.19 -14.47 OLGAFS 70
71 YASARA                   -12.36 -7.45 -11.76                   -15.92 -10.19 -14.47 YASARA 71
72 keasar−server                   -12.36 -7.45 -11.76                   -15.92 -10.19 -14.47 keasar−server 72
73 mahmood−torda−server                   -12.36 -7.45 -11.76                   -15.92 -10.19 -14.47 mahmood−torda−server 73
74 test_http_server_01                   -12.36 -7.45 -11.76                   -15.92 -10.19 -14.47 test_http_server_01 74