T0485

X-ray Targets
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T0485

S-adenosyl-L-methionine-dependent methyltransferase from Methanococcus maripaludis

Target type: Server only

Target sequence:

>T0485 Putative S-adenosyl-L-methionine-dependent Methyltransferase, Methanococcus maripaludis, 218 residues
MSENKKKFDKKGAKNMDEISKTLFAPIYPIIAENIINRFGITAGNCIDIGSGPGALSIALAKQSDFSIRALDFSKHMNEIALKNIADADLNDRIQIVQGDVHNIPIEDNYADLIVSRGSVFFWEDVTTAFREIYRILKSGGKTYIGGGFGNKELRDSISAEMIRKNPDWKEFNRKNISQENVERFQNVLDEIGVSSYEIILEDEGFWIIISKTDQEVI

Structure:
Method: X-ray, res=1.15Å, R/Rfree=0.12/0.14
Determined by: JCSG
PDB ID: 3dlc

PyMOL of 3dlc

Domains:  PyMOL of domains

Single domain protein.

To compute the weighted sum, GDT-TS for each domain was multiplied by the domain length, and this sum was divided by the sum of domain lengths. Each point represents first server model. Green, gray and black points are top 10, bottom 25% and the rest of prediction models. Blue line is the best-fit slope line (intersection 0) to the top 10 server models. Red line is the diagonal. Slope and root mean square y-x distance for the top 10 models (average difference between the domain GDT-TS scores and the whole chain GDT-TS score) are shown above the plot.

Structure classification:

SAM-dependent methyltransferase fold.

CASP category:

Comparative modeling:hard.

Closest templates:

1im8.

Target sequence - PDB file inconsistencies:

T0485    3dlc.pdb    T0485.pdb    PyMOL    PyMOL of domains   

Residue change log: change 45 T to N; change 89 N to D; change 127 A to T; change 194 I to V; change 202 G to E; change 1, 16, 77, 162, MSE to MET; remove 0 G as it is not present in target sequence;

We suggest to evaluate this target as a single domain spanning whole chain. However, N-terminal segment extends away and may be removed, resulting in this domain definition:

1st domain: target 5-216 ; pdb 5-216

Sequence classification:

Methyltransferase domain Methyltransf_11 in Pfam.

Server predictions:

T0485:pdb 1-218:seq 1-218:CM_hard;   alignment

485_1:pdb 5-216:seq 5-216:CM_hard;   alignment

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 ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ ↓ GROUP #
T0485 485_1 T0485 485_1 T0485 485_1 T0485 485_1
First score First Z-score Best score Best Z-score
1 pro−sp3−TASSER 66.74 63.69 71.52 68.51 65.37 71.71 2.16 2.95 2.25 2.17 3.09 2.26 66.74 63.69 71.52 68.51 65.37 71.71 2.08 2.88 2.19 2.09 2.86 2.21 pro−sp3−TASSER 1
2 RAPTOR 66.63 59.82 70.43 68.51 61.52 70.64 2.14 2.28 2.10 2.17 2.42 2.11 66.63 59.82 70.43 68.51 61.52 70.64 2.06 2.08 2.02 2.09 2.09 2.04 RAPTOR 2
3 Zhang−Server 64.68 54.89 67.90 66.27 56.21 68.32 1.81 1.42 1.75 1.81 1.50 1.78 68.00 63.49 72.25 69.81 66.75 72.60 2.32 2.84 2.31 2.33 3.14 2.36 Zhang−Server 3
4 pipe_int 63.07 54.28 68.35 64.74 55.31 69.04 1.55 1.32 1.81 1.56 1.35 1.88 63.07 54.28 68.35 64.74 55.31 69.04 1.37 0.95 1.69 1.37 0.85 1.78 pipe_int 4
5 BioSerf 62.62 49.47 65.41 64.39 52.12 65.66 1.47 0.48 1.41 1.50 0.79 1.41 62.62 49.47 65.41 64.39 52.12 65.66 1.28 -0.04 1.23 1.31 0.21 1.23 BioSerf 5
6 SAM−T08−server 61.70 57.88 64.59 63.21 59.20 64.81 1.32 1.94 1.30 1.31 2.02 1.29 61.70 57.88 64.59 63.21 59.20 64.81 1.10 1.68 1.10 1.08 1.63 1.10 SAM−T08−server 6
7 FEIG 61.70 57.11 66.35 63.56 54.13 66.69 1.32 1.81 1.54 1.37 1.14 1.56 61.70 57.11 67.20 63.56 56.88 67.62 1.10 1.53 1.51 1.15 1.16 1.55 FEIG 7
8 LEE−SERVER 61.35 50.69 67.76 62.97 52.01 67.85 1.26 0.69 1.73 1.27 0.77 1.72 61.35 51.45 68.52 62.97 52.79 68.71 1.03 0.36 1.72 1.04 0.34 1.73 LEE−SERVER 8
9 METATASSER 61.01 53.67 66.20 62.85 54.21 66.63 1.20 1.21 1.52 1.25 1.15 1.55 67.55 64.11 69.48 69.46 65.92 69.68 2.24 2.96 1.87 2.27 2.97 1.88 METATASSER 9
10 COMA−M 60.66 50.27 57.96 62.38 51.69 58.17 1.15 0.62 0.38 1.17 0.72 0.37 60.66 52.33 57.96 62.38 53.70 58.17 0.90 0.55 0.05 0.93 0.52 0.02 COMA−M 10
11 Pcons_multi 59.98 50.19 60.31 61.67 49.65 60.32 1.03 0.61 0.71 1.06 0.36 0.67 59.98 53.21 60.77 61.67 54.99 60.76 0.77 0.73 0.49 0.79 0.78 0.44 Pcons_multi 11
12 fais−server 59.52 51.95 60.98 60.02 51.45 61.16 0.96 0.91 0.80 0.79 0.68 0.78 59.52 51.95 60.98 60.02 53.34 61.16 0.68 0.47 0.52 0.48 0.45 0.51 fais−server 12
13 3DShot2 58.60 48.81 55.65 60.26 50.20 56.04 0.80 0.37 0.06 0.83 0.46 0.07 58.60 48.81 55.65 60.26 50.20 56.04 0.50 -0.18 -0.32 0.52 -0.18 -0.32 3DShot2 13
14 BAKER−ROBETTA 58.14 51.11 60.49 59.55 51.69 60.72 0.73 0.77 0.73 0.71 0.72 0.72 59.29 51.19 64.50 60.61 54.17 64.53 0.63 0.31 1.08 0.59 0.62 1.05 BAKER−ROBETTA 14
15 COMA 58.14 50.19 56.09 59.43 50.43 56.18 0.73 0.61 0.13 0.69 0.50 0.09 58.14 50.19 57.96 59.55 50.43 58.17 0.41 0.11 0.05 0.39 -0.13 0.02 COMA 15
16 Phyre_de_novo 57.45 51.80 58.77 59.08 53.26 58.90 0.61 0.88 0.49 0.64 0.99 0.47 57.45 51.80 58.77 59.08 53.26 58.90 0.28 0.44 0.18 0.30 0.44 0.14 Phyre_de_novo 16
17 FFASflextemplate 57.34 52.68 58.16 58.96 54.17 58.91 0.59 1.04 0.41 0.62 1.15 0.47 57.34 52.68 58.16 58.96 54.17 58.91 0.25 0.62 0.08 0.28 0.62 0.14 FFASflextemplate 17
18 HHpred2 57.23 50.12 60.56 58.49 50.35 60.62 0.58 0.59 0.74 0.54 0.48 0.71 57.23 50.12 60.56 58.49 50.35 60.62 0.23 0.09 0.46 0.19 -0.15 0.42 HHpred2 18
19 HHpred4 57.11 45.87 59.31 58.26 46.85 59.50 0.56 -0.14 0.57 0.50 -0.12 0.55 57.11 45.87 59.31 58.26 46.85 59.50 0.21 -0.78 0.26 0.14 -0.85 0.24 HHpred4 19
20 PS2−server 56.54 48.81 62.11 58.02 48.19 62.27 0.46 0.37 0.95 0.46 0.11 0.94 58.37 52.26 62.11 59.91 53.54 62.27 0.45 0.53 0.70 0.46 0.49 0.68 PS2−server 20
21 GeneSilicoMetaServer 56.19 51.30 54.30 57.90 52.87 54.94 0.40 0.80 -0.12 0.44 0.92 -0.09 56.42 51.30 54.30 58.02 52.87 54.94 0.08 0.33 -0.53 0.10 0.36 -0.50 GeneSilicoMetaServer 21
22 3D−JIGSAW_AEP 55.96 46.29 52.32 56.84 48.07 52.97 0.36 -0.07 -0.39 0.27 0.09 -0.36 58.60 46.33 55.05 59.67 49.21 55.71 0.50 -0.69 -0.41 0.41 -0.38 -0.38 3D−JIGSAW_AEP 22
23 FALCON_CONSENSUS 55.85 48.59 55.65 57.31 49.84 55.96 0.35 0.33 0.06 0.35 0.40 0.06 57.11 48.59 56.94 58.14 49.84 57.28 0.21 -0.22 -0.11 0.12 -0.25 -0.12 FALCON_CONSENSUS 23
24 PSI 55.73 50.46 58.10 57.19 51.77 58.21 0.33 0.65 0.40 0.33 0.73 0.37 57.57 51.87 59.17 59.32 52.95 59.53 0.30 0.45 0.24 0.35 0.37 0.24 PSI 24
25 MULTICOM−RANK 55.39 46.29 55.44 56.60 47.01 55.52 0.27 -0.07 0.04 0.23 -0.10 -0.00 64.45 58.18 63.51 66.27 59.51 63.67 1.63 1.75 0.93 1.66 1.69 0.91 MULTICOM−RANK 25
26 Pcons_local 55.27 51.15 52.62 56.84 52.59 53.16 0.25 0.77 -0.35 0.27 0.87 -0.33 55.27 51.15 52.62 56.84 52.59 53.16 -0.15 0.30 -0.80 -0.13 0.30 -0.79 Pcons_local 26
27 Pcons_dot_net 55.27 51.15 52.62 56.84 52.59 53.16 0.25 0.77 -0.35 0.27 0.87 -0.33 59.29 51.19 64.50 60.61 54.17 64.53 0.63 0.31 1.08 0.59 0.62 1.05 Pcons_dot_net 27
28 HHpred5 55.27 49.54 60.17 56.60 50.94 60.33 0.25 0.49 0.69 0.23 0.59 0.67 55.27 49.54 60.17 56.60 50.94 60.33 -0.15 -0.03 0.40 -0.17 -0.03 0.37 HHpred5 28
29 MUProt 55.27 45.38 58.51 56.72 45.24 58.82 0.25 -0.23 0.46 0.25 -0.40 0.46 55.27 48.70 61.23 56.72 50.08 61.52 -0.15 -0.20 0.56 -0.15 -0.20 0.56 MUProt 29
30 MULTICOM−CLUSTER 55.27 44.65 55.23 56.37 45.52 55.32 0.25 -0.36 0.01 0.20 -0.35 -0.03 64.45 57.95 63.51 66.27 59.51 63.67 1.63 1.70 0.93 1.66 1.69 0.91 MULTICOM−CLUSTER 30
31 SAM−T02−server 55.05 50.31 52.22 56.60 51.73 53.07 0.21 0.63 -0.41 0.23 0.72 -0.35 55.16 50.31 52.22 56.72 51.73 53.07 -0.17 0.13 -0.86 -0.15 0.13 -0.80 SAM−T02−server 31
32 MULTICOM−REFINE 55.05 48.24 55.42 56.37 44.26 55.51 0.21 0.27 0.03 0.20 -0.57 -0.01 55.27 48.36 60.04 56.72 49.73 60.27 -0.15 -0.27 0.38 -0.15 -0.27 0.36 MULTICOM−REFINE 32
33 Frankenstein 54.82 49.77 54.38 56.37 51.18 54.59 0.18 0.53 -0.11 0.20 0.63 -0.13 54.82 49.77 57.03 56.37 51.18 57.27 -0.24 0.02 -0.10 -0.21 0.02 -0.12 Frankenstein 33
34 MULTICOM−CMFR 54.82 45.87 58.44 56.37 45.48 58.76 0.18 -0.14 0.45 0.20 -0.36 0.45 55.73 48.93 58.44 56.96 50.31 58.76 -0.06 -0.15 0.12 -0.10 -0.16 0.12 MULTICOM−CMFR 34
35 GS−KudlatyPred 54.47 47.44 61.19 55.90 48.66 61.41 0.12 0.13 0.83 0.12 0.19 0.82 55.73 49.31 61.19 57.08 51.49 61.41 -0.06 -0.07 0.56 -0.08 0.08 0.55 GS−KudlatyPred 35
36 SAM−T06−server 54.36 47.63 57.58 55.54 48.62 57.80 0.10 0.16 0.33 0.06 0.18 0.31 54.70 47.63 57.58 56.25 48.78 57.80 -0.26 -0.42 -0.01 -0.24 -0.46 -0.04 SAM−T06−server 36
37 FFASsuboptimal 53.90 50.08 49.45 55.42 51.49 50.29 0.02 0.59 -0.79 0.04 0.68 -0.73 53.90 50.08 49.45 55.42 51.49 50.29 -0.41 0.08 -1.30 -0.39 0.08 -1.25 FFASsuboptimal 37
38 FAMSD 53.67 44.84 58.65 54.95 45.09 58.90 -0.02 -0.32 0.48 -0.04 -0.43 0.47 54.36 49.47 58.65 55.90 50.87 58.90 -0.32 -0.04 0.16 -0.30 -0.04 0.14 FAMSD 38
39 circle 53.67 44.57 58.06 54.95 43.63 58.23 -0.02 -0.37 0.40 -0.04 -0.68 0.37 53.67 46.98 58.06 54.95 48.31 58.23 -0.46 -0.55 0.06 -0.48 -0.56 0.03 circle 39
40 nFOLD3 53.10 46.22 56.64 54.60 47.52 56.79 -0.11 -0.08 0.20 -0.09 -0.01 0.17 55.73 48.74 58.13 57.31 50.12 58.43 -0.06 -0.19 0.07 -0.04 -0.19 0.06 nFOLD3 40
41 keasar−server 53.10 45.11 50.39 54.72 46.50 50.65 -0.11 -0.28 -0.66 -0.07 -0.18 -0.68 56.77 50.00 57.21 58.37 51.53 57.50 0.14 0.07 -0.07 0.16 0.09 -0.09 keasar−server 41
42 CpHModels 52.52 47.25 49.82 54.01 48.59 50.66 -0.21 0.10 -0.74 -0.19 0.18 -0.68 52.52 47.25 49.82 54.01 48.59 50.66 -0.68 -0.50 -1.24 -0.66 -0.50 -1.19 CpHModels 42
43 LOOPP_Server 52.18 44.38 53.01 53.66 45.64 53.86 -0.26 -0.40 -0.30 -0.25 -0.33 -0.24 52.18 44.38 53.01 53.66 45.64 53.86 -0.75 -1.09 -0.74 -0.73 -1.09 -0.68 LOOPP_Server 43
44 FALCON 51.61 43.42 52.86 52.59 44.18 53.11 -0.36 -0.57 -0.32 -0.42 -0.59 -0.34 57.11 48.59 56.94 58.14 49.84 57.28 0.21 -0.22 -0.11 0.12 -0.25 -0.12 FALCON 44
45 RBO−Proteus 51.03 48.28 62.13 52.36 49.53 62.49 -0.45 0.27 0.96 -0.46 0.34 0.97 51.03 48.28 63.11 52.36 49.53 63.47 -0.97 -0.29 0.86 -0.98 -0.31 0.88 RBO−Proteus 45
46 YASARA 50.80 44.46 56.38 52.12 45.60 56.59 -0.49 -0.39 0.17 -0.50 -0.34 0.15 51.72 48.70 57.62 53.07 50.08 57.86 -0.84 -0.20 -0.01 -0.84 -0.20 -0.03 YASARA 46
47 GS−MetaServer2 49.20 42.77 43.75 50.59 43.99 44.58 -0.76 -0.68 -1.57 -0.75 -0.62 -1.53 56.31 50.96 52.31 57.90 52.40 53.16 0.05 0.26 -0.85 0.08 0.26 -0.79 GS−MetaServer2 47
48 MUFOLD−Server 48.51 41.40 51.83 50.12 42.81 52.25 -0.87 -0.92 -0.46 -0.82 -0.82 -0.46 49.77 44.30 51.83 50.94 45.32 52.25 -1.22 -1.10 -0.92 -1.24 -1.16 -0.94 MUFOLD−Server 48
49 FFASstandard 47.82 44.61 46.73 49.17 45.87 47.44 -0.99 -0.36 -1.16 -0.98 -0.29 -1.13 53.10 48.89 53.32 54.60 50.27 54.17 -0.57 -0.16 -0.69 -0.55 -0.16 -0.63 FFASstandard 49
50 MUSTER 47.36 42.62 52.95 48.82 43.95 53.30 -1.06 -0.71 -0.31 -1.04 -0.63 -0.31 56.88 48.74 60.18 58.49 50.12 60.42 0.16 -0.19 0.40 0.19 -0.19 0.39 MUSTER 50
51 mGenTHREADER 47.25 39.95 46.70 48.59 41.08 47.54 -1.08 -1.17 -1.17 -1.07 -1.13 -1.12 47.25 39.95 46.70 48.59 41.08 47.54 -1.71 -2.00 -1.73 -1.69 -2.01 -1.70 mGenTHREADER 51
52 Pushchino 46.90 42.01 37.66 48.23 43.20 38.49 -1.14 -0.81 -2.41 -1.13 -0.76 -2.38 46.90 42.01 37.66 48.23 43.20 38.49 -1.77 -1.57 -3.16 -1.76 -1.58 -3.16 Pushchino 52
53 FUGUE_KM 46.45 41.09 43.54 47.76 42.26 44.38 -1.22 -0.97 -1.60 -1.21 -0.92 -1.56 46.45 41.09 43.54 47.76 42.26 44.38 -1.86 -1.76 -2.23 -1.85 -1.77 -2.21 FUGUE_KM 53
54 ACOMPMOD 46.10 43.20 44.87 47.41 44.42 45.50 -1.27 -0.61 -1.42 -1.26 -0.55 -1.40 46.10 43.20 44.87 47.41 44.42 45.50 -1.93 -1.33 -2.02 -1.91 -1.34 -2.03 ACOMPMOD 54
55 3D−JIGSAW_V3 46.10 32.84 48.85 47.29 33.65 49.17 -1.27 -2.40 -0.87 -1.28 -2.42 -0.89 46.79 35.24 49.25 47.88 36.01 49.56 -1.80 -2.96 -1.33 -1.82 -3.02 -1.37 3D−JIGSAW_V3 55
56 Phragment 44.95 34.25 47.35 46.23 35.14 47.71 -1.46 -2.16 -1.08 -1.46 -2.16 -1.09 50.57 45.91 52.53 52.01 47.21 52.94 -1.06 -0.77 -0.81 -1.04 -0.78 -0.82 Phragment 56
57 Phyre2 44.61 35.05 46.49 45.76 35.93 46.86 -1.52 -2.02 -1.20 -1.53 -2.02 -1.21 51.72 47.29 53.17 53.18 48.62 53.59 -0.84 -0.49 -0.71 -0.82 -0.49 -0.72 Phyre2 57
58 Poing 44.27 34.71 47.15 45.52 35.69 47.53 -1.58 -2.08 -1.11 -1.57 -2.06 -1.12 51.15 46.56 52.73 52.59 47.88 53.12 -0.95 -0.64 -0.78 -0.93 -0.64 -0.80 Poing 58
59 panther_server 43.23 38.34 43.10 44.46 39.43 43.82 -1.75 -1.45 -1.66 -1.75 -1.41 -1.64 56.77 48.81 50.57 58.37 50.20 51.14 0.14 -0.18 -1.12 0.16 -0.18 -1.12 panther_server 59
60 Distill 42.20 37.23 47.54 43.40 38.29 47.88 -1.92 -1.64 -1.05 -1.92 -1.61 -1.07 43.23 38.88 48.04 44.46 39.98 48.18 -2.49 -2.22 -1.52 -2.47 -2.23 -1.59 Distill 60
61 rehtnap 41.40 35.97 37.24 42.57 36.99 38.06 -2.05 -1.86 -2.47 -2.05 -1.84 -2.44 53.33 48.05 43.79 54.84 49.41 44.63 -0.52 -0.33 -2.19 -0.50 -0.34 -2.17 rehtnap 61
62 Fiser−M4T 40.14 37.77 24.83 41.27 38.84 25.63 -2.26 -1.55 -4.18 -2.27 -1.51 -4.18 40.14 37.77 24.83 41.27 38.84 25.63 -3.09 -2.44 -5.19 -3.08 -2.45 -5.24 Fiser−M4T 62
63 FOLDpro 38.65 35.47 40.54 39.74 36.48 40.69 -2.51 -1.95 -2.02 -2.51 -1.92 -2.07 38.65 35.47 40.54 39.74 36.48 40.69 -3.38 -2.92 -2.71 -3.37 -2.93 -2.81 FOLDpro 63
64 3Dpro 37.62 28.75 38.14 38.68 29.56 38.25 -2.68 -3.11 -2.35 -2.69 -3.13 -2.42 42.55 40.86 46.87 43.75 42.02 47.09 -2.62 -1.81 -1.71 -2.61 -1.82 -1.77 3Dpro 64
65 MUFOLD−MD 25.46 22.44 47.50 26.18 23.07 47.81 -4.70 -4.21 -1.06 -4.72 -4.25 -1.08 43.58 40.90 57.43 44.81 42.06 57.83 -2.42 -1.80 -0.04 -2.41 -1.81 -0.03 MUFOLD−MD 65
66 mariner1 15.60 12.00 7.34 16.04 12.34 8.12 -6.34 -6.02 -6.59 -6.38 -6.12 -6.62 52.18 43.39 52.04 53.66 44.62 52.88 -0.75 -1.29 -0.89 -0.73 -1.30 -0.83 mariner1 66
67 RANDOM 12.63 10.65 12.63 13.36 11.33 13.36 -6.83 -6.26 -5.86 -6.81 -6.29 -5.89 12.63 10.65 12.63 13.36 11.33 13.36 -8.43 -8.01 -7.12 -8.37 -7.97 -7.23 RANDOM 67
68 mahmood−torda−server 11.01 8.45 15.68 11.44 8.80 15.67 -7.10 -6.64 -5.44 -7.13 -6.73 -5.57 12.62 10.13 15.68 12.97 10.42 15.67 -8.43 -8.12 -6.64 -8.45 -8.15 -6.85 mahmood−torda−server 68
69 schenk−torda−server 10.21 9.21 14.01 10.61 9.59 14.26 -7.24 -6.51 -5.67 -7.26 -6.59 -5.77 10.89 9.90 14.01 11.32 10.10 14.26 -8.77 -8.16 -6.90 -8.76 -8.22 -7.08 schenk−torda−server 69
70 OLGAFS 7.80 7.03 -4.68 8.02 7.23 -3.92 -7.64 -6.88 -8.25 -7.68 -7.00 -8.30 8.49 7.03 -4.68 8.73 7.23 -3.92 -9.23 -8.75 -9.86 -9.25 -8.79 -10.02 OLGAFS 70
71 BHAGEERATH                                     -6.83 -6.26 -5.86 -6.81 -6.29 -5.89                                     -8.43 -8.01 -7.12 -8.37 -7.97 -7.23 BHAGEERATH 71
72 forecast                                     -6.83 -6.26 -5.86 -6.81 -6.29 -5.89                                     -8.43 -8.01 -7.12 -8.37 -7.97 -7.23 forecast 72
73 huber−torda−server                                     -6.83 -6.26 -5.86 -6.81 -6.29 -5.89                                     -8.43 -8.01 -7.12 -8.37 -7.97 -7.23 huber−torda−server 73
74 test_http_server_01                                     -6.83 -6.26 -5.86 -6.81 -6.29 -5.89                                     -8.43 -8.01 -7.12 -8.37 -7.97 -7.23 test_http_server_01 74