T0488

X-ray Targets
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T0488

second PDZ domain of the NUMB-binding protein 2 from Homo sapiens

Target type: Server only

Target sequence:

>T0488 LNX2A@3, Homo sapiens, 95 residues
SMEILQVALHKRDSGEQLGIKLVRRTDEPGVFILDLLEGGLAAQDGRLSSNDRVLAINGHDLKYGTPELAAQIIQASGERVNLTIARPGKPEIEL

Structure:
Method: X-ray, res=1.3Å, R/Rfree=0.14/0.18
Determined by: SGC
PDB ID: 2vwr

PyMOL of 2vwr

Domains:  PyMOL of domains

Single domain protein. However, C-terminal segment of this structure protrudes away and interacts with the peptide-binding site of a symmetry mate. This segments (424-428) should be removed for domain-based evaluation.

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:

PDZ domain fold.

CASP category:

Whole chain: Comparative modeling:easy.

Domain (with C-terminal 424-428 removed): Comparative modeling:easy.

Closest templates:

1d5g, 1m5z, 2fe5, 1um1, 2daz.

Target sequence - PDB file inconsistencies:

T0488    2vwr.pdb    T0488.pdb    PyMOL    PyMOL of domains   

We suggest to evaluate this target as a single domain spanning whole chain. However, C-terminal segment of this structure protrudes away and interacts with the peptide-binding site of a symmetry mate. This segments (A:424-A:428) can be removed for domain-based evaluation, resulting this domain definition:

1st domain: target 1-90 ; pdb -1-423

Sequence classification:

PDZ domain in Pfam.

Server predictions:

T0488:pdb -1-428:seq 1-95:CM_easy;   alignment

488_1:pdb -1-423:seq 1-90:CM_easy;   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 #
T0488 488_1 T0488 488_1 T0488 488_1 T0488 488_1
First score First Z-score Best score Best Z-score
1 YASARA 89.47 87.54 90.58 93.33 91.30 90.92 1.86 1.72 1.38 1.88 1.66 1.34 89.47 87.54 90.58 93.33 91.30 90.92 1.72 1.59 1.29 1.78 1.55 1.23 YASARA 1
2 RAPTOR 87.63 85.17 90.84 91.39 88.80 91.36 1.43 1.36 1.44 1.43 1.29 1.44 88.16 85.70 90.84 91.39 91.02 91.36 1.37 1.24 1.35 1.26 1.49 1.35 RAPTOR 2
3 pipe_int 87.37 83.51 89.09 90.56 86.48 89.68 1.37 1.11 1.07 1.24 0.95 1.07 87.37 85.44 89.54 90.56 88.80 90.01 1.16 1.19 1.01 1.03 1.07 0.99 pipe_int 3
4 BAKER−ROBETTA 86.84 80.88 89.13 90.00 87.04 89.73 1.25 0.71 1.08 1.11 1.03 1.08 86.84 84.21 89.13 90.00 87.50 89.73 1.02 0.96 0.91 0.88 0.83 0.91 BAKER−ROBETTA 4
5 PS2−server 86.58 85.88 89.74 90.83 90.09 90.07 1.19 1.47 1.20 1.30 1.48 1.16 86.58 85.88 89.74 90.83 90.09 90.07 0.95 1.28 1.07 1.10 1.32 1.00 PS2−server 5
6 MUSTER 86.58 83.95 90.33 90.00 87.22 90.53 1.19 1.18 1.33 1.11 1.06 1.26 86.58 83.95 90.33 90.00 87.22 90.53 0.95 0.91 1.22 0.88 0.78 1.13 MUSTER 6
7 MULTICOM−CLUSTER 86.32 84.56 89.65 89.72 88.24 90.17 1.13 1.27 1.19 1.04 1.21 1.18 88.16 84.56 91.37 90.56 88.33 92.11 1.37 1.03 1.49 1.03 0.98 1.55 MULTICOM−CLUSTER 7
8 BioSerf 86.05 86.05 88.38 90.28 90.28 88.75 1.07 1.49 0.92 1.17 1.51 0.87 86.05 86.05 88.38 90.28 90.28 88.75 0.81 1.31 0.71 0.96 1.35 0.65 BioSerf 8
9 keasar−server 86.05 79.74 88.09 89.17 87.13 88.56 1.07 0.54 0.86 0.92 1.05 0.83 86.32 84.39 89.51 90.00 89.07 90.22 0.88 0.99 1.01 0.88 1.12 1.04 keasar−server 9
10 Phragment 85.79 84.39 88.76 89.44 87.96 89.44 1.01 1.24 1.00 0.98 1.17 1.02 85.79 84.39 88.76 89.44 87.96 89.44 0.74 0.99 0.81 0.73 0.91 0.83 Phragment 10
11 Zhang−Server 85.79 80.88 87.65 89.17 83.98 88.26 1.01 0.71 0.76 0.92 0.58 0.76 85.79 81.40 87.70 89.17 85.00 88.38 0.74 0.42 0.53 0.65 0.36 0.55 Zhang−Server 11
12 Poing 85.53 84.12 88.76 89.44 87.96 89.48 0.95 1.20 1.00 0.98 1.17 1.03 85.53 84.12 88.76 89.44 87.96 89.48 0.67 0.94 0.81 0.73 0.91 0.84 Poing 12
13 Phyre2 85.53 84.12 88.83 89.44 87.96 89.47 0.95 1.20 1.01 0.98 1.17 1.03 85.53 84.12 88.83 89.44 87.96 89.47 0.67 0.94 0.83 0.73 0.91 0.84 Phyre2 13
14 Phyre_de_novo 85.53 82.72 87.65 88.61 86.02 87.91 0.95 0.99 0.76 0.79 0.88 0.69 85.53 82.72 88.41 89.44 86.85 88.90 0.67 0.68 0.72 0.73 0.71 0.69 Phyre_de_novo 14
15 RBO−Proteus 85.53 72.46 86.97 89.72 75.93 87.25 0.95 -0.55 0.62 1.04 -0.60 0.54 85.53 72.81 87.93 89.72 76.57 88.21 0.67 -1.21 0.59 0.80 -1.24 0.50 RBO−Proteus 15
16 LOOPP_Server 85.26 80.00 87.28 89.44 76.11 88.39 0.88 0.58 0.68 0.98 -0.57 0.79 85.26 80.00 87.28 89.44 76.11 88.39 0.60 0.16 0.42 0.73 -1.32 0.55 LOOPP_Server 16
17 FALCON 85.26 79.83 84.58 88.61 82.87 85.36 0.88 0.56 0.11 0.79 0.42 0.13 85.26 79.83 84.58 88.61 82.87 85.36 0.60 0.13 -0.28 0.50 -0.05 -0.27 FALCON 17
18 SAM−T08−server 84.74 82.98 88.58 89.44 87.22 88.92 0.76 1.03 0.96 0.98 1.06 0.91 87.11 85.70 89.86 90.56 88.33 90.20 1.09 1.24 1.10 1.03 0.98 1.04 SAM−T08−server 18
19 FAMSD 84.74 82.63 88.18 88.89 86.67 88.62 0.76 0.98 0.87 0.85 0.98 0.84 84.74 82.63 88.18 88.89 86.67 88.62 0.46 0.66 0.66 0.58 0.67 0.61 FAMSD 19
20 MUProt 84.74 77.02 88.78 87.22 74.44 89.26 0.76 0.13 1.00 0.46 -0.82 0.98 84.74 82.63 88.78 87.22 85.37 89.26 0.46 0.66 0.81 0.12 0.43 0.78 MUProt 20
21 mGenTHREADER 84.47 84.12 86.75 88.61 88.24 87.97 0.70 1.20 0.57 0.79 1.21 0.70 84.47 84.12 86.75 88.61 88.24 87.97 0.39 0.94 0.28 0.50 0.97 0.44 mGenTHREADER 21
22 MULTICOM−REFINE 84.47 74.91 88.46 87.22 78.52 88.74 0.70 -0.18 0.93 0.46 -0.22 0.87 84.74 83.33 88.66 87.50 78.89 88.96 0.46 0.79 0.78 0.20 -0.80 0.70 MULTICOM−REFINE 22
23 Pushchino 83.95 82.89 85.25 87.78 86.67 86.46 0.58 1.02 0.25 0.59 0.98 0.37 83.95 82.89 85.25 87.78 86.67 86.46 0.25 0.71 -0.11 0.28 0.67 0.03 Pushchino 23
24 pro−sp3−TASSER 83.95 78.86 84.80 86.67 74.07 85.67 0.58 0.41 0.16 0.34 -0.87 0.20 87.63 85.00 89.08 90.83 89.35 89.78 1.23 1.11 0.89 1.10 1.18 0.92 pro−sp3−TASSER 24
25 MULTICOM−RANK 83.68 74.74 87.48 86.67 77.78 87.67 0.52 -0.21 0.73 0.34 -0.33 0.63 83.95 78.95 87.90 86.94 82.96 88.23 0.25 -0.04 0.58 0.05 -0.03 0.51 MULTICOM−RANK 25
26 MUFOLD−Server 83.68 65.09 83.66 88.06 68.43 84.21 0.52 -1.66 -0.08 0.66 -1.70 -0.12 83.68 75.97 84.39 88.06 80.46 84.82 0.18 -0.61 -0.33 0.35 -0.50 -0.41 MUFOLD−Server 26
27 METATASSER 83.42 72.28 85.81 86.39 78.33 86.83 0.45 -0.58 0.37 0.27 -0.25 0.45 85.26 76.93 86.78 89.17 79.54 87.22 0.60 -0.43 0.29 0.65 -0.68 0.23 METATASSER 27
28 HHpred5 83.16 82.46 85.10 87.22 86.48 85.58 0.39 0.95 0.22 0.46 0.95 0.18 83.16 82.46 85.10 87.22 86.48 85.58 0.04 0.63 -0.15 0.12 0.64 -0.21 HHpred5 28
29 Distill 83.16 80.35 78.59 85.28 83.06 78.91 0.39 0.63 -1.15 0.02 0.45 -1.28 83.16 82.11 80.34 85.56 85.00 80.66 0.04 0.56 -1.39 -0.33 0.36 -1.54 Distill 29
30 huber−torda−server 83.16 70.26 85.22 86.94 85.83 86.52 0.39 -0.88 0.25 0.40 0.86 0.38 83.16 72.02 85.22 86.94 85.83 86.52 0.04 -1.36 -0.12 0.05 0.51 0.04 huber−torda−server 30
31 GS−KudlatyPred 82.89 77.63 87.03 87.22 81.67 87.58 0.33 0.22 0.63 0.46 0.24 0.61 83.95 79.56 87.94 88.33 83.70 88.47 0.25 0.07 0.59 0.43 0.11 0.57 GS−KudlatyPred 31
32 Pcons_local 82.37 81.67 84.98 86.94 86.20 86.62 0.21 0.83 0.20 0.40 0.91 0.41 82.37 81.67 84.98 86.94 86.20 86.62 -0.17 0.48 -0.18 0.05 0.58 0.07 Pcons_local 32
33 Pcons_dot_net 82.37 81.67 84.98 86.94 86.20 86.62 0.21 0.83 0.20 0.40 0.91 0.41 85.00 83.77 87.63 89.17 88.43 89.27 0.53 0.88 0.51 0.65 1.00 0.79 Pcons_dot_net 33
34 Pcons_multi 82.37 81.67 84.98 86.94 86.20 86.62 0.21 0.83 0.20 0.40 0.91 0.41 87.11 82.89 89.97 91.11 86.20 89.99 1.09 0.71 1.13 1.18 0.58 0.98 Pcons_multi 34
35 ACOMPMOD 82.11 76.32 83.82 86.67 80.56 85.46 0.15 0.03 -0.05 0.34 0.08 0.15 82.11 76.32 85.45 86.67 80.56 86.03 -0.24 -0.54 -0.06 -0.02 -0.48 -0.09 ACOMPMOD 35
36 CpHModels 81.84 80.44 82.19 86.39 84.91 83.83 0.09 0.65 -0.39 0.27 0.72 -0.20 81.84 80.44 82.19 86.39 84.91 83.83 -0.31 0.24 -0.91 -0.10 0.34 -0.68 CpHModels 36
37 LEE−SERVER 81.32 79.56 87.07 85.83 83.98 87.44 -0.03 0.52 0.64 0.14 0.58 0.58 87.11 81.49 89.96 90.28 89.17 90.40 1.09 0.44 1.12 0.96 1.14 1.09 LEE−SERVER 37
38 FEIG 81.05 78.42 83.93 85.00 82.22 84.44 -0.10 0.34 -0.02 -0.05 0.33 -0.07 84.47 78.42 85.42 88.33 82.22 85.90 0.39 -0.14 -0.06 0.43 -0.17 -0.12 FEIG 38
39 MULTICOM−CMFR 81.05 77.02 86.63 85.56 81.30 86.91 -0.10 0.13 0.55 0.08 0.19 0.47 81.84 77.02 86.63 86.39 81.30 86.91 -0.31 -0.41 0.25 -0.10 -0.34 0.15 MULTICOM−CMFR 39
40 fais−server 80.53 75.26 82.84 83.89 78.89 83.30 -0.22 -0.13 -0.25 -0.31 -0.16 -0.32 86.84 86.49 89.09 90.28 89.91 89.48 1.02 1.39 0.90 0.96 1.28 0.84 fais−server 40
41 HHpred4 80.26 73.95 81.84 83.61 77.50 82.05 -0.28 -0.33 -0.47 -0.37 -0.37 -0.59 80.26 73.95 81.84 83.61 77.50 82.05 -0.73 -0.99 -1.00 -0.86 -1.06 -1.16 HHpred4 41
42 HHpred2 80.26 72.54 84.02 83.89 79.44 84.15 -0.28 -0.54 -0.01 -0.31 -0.08 -0.13 80.26 72.54 84.02 83.89 79.44 84.15 -0.73 -1.26 -0.43 -0.78 -0.70 -0.60 HHpred2 42
43 forecast 80.00 77.54 86.57 84.44 81.85 87.24 -0.34 0.21 0.53 -0.18 0.27 0.54 80.00 77.54 86.57 84.44 81.85 87.24 -0.80 -0.31 0.24 -0.63 -0.24 0.24 forecast 43
44 COMA−M 79.47 69.74 82.24 83.06 72.59 82.94 -0.46 -0.96 -0.38 -0.50 -1.09 -0.40 80.26 73.42 82.65 83.89 76.48 83.03 -0.73 -1.09 -0.79 -0.78 -1.25 -0.90 COMA−M 44
45 Frankenstein 79.21 73.42 84.01 83.33 77.22 84.45 -0.52 -0.41 -0.01 -0.44 -0.41 -0.07 81.58 75.44 86.40 85.00 79.63 86.99 -0.38 -0.71 0.19 -0.48 -0.66 0.17 Frankenstein 45
46 3D−JIGSAW_V3 78.68 73.07 82.88 82.78 78.52 83.30 -0.65 -0.46 -0.25 -0.56 -0.22 -0.32 79.47 74.03 83.58 83.33 78.52 84.39 -0.94 -0.98 -0.55 -0.93 -0.87 -0.53 3D−JIGSAW_V3 46
47 PSI 78.68 70.79 81.63 83.06 74.72 83.26 -0.65 -0.80 -0.51 -0.50 -0.78 -0.33 79.74 76.58 84.25 83.89 80.56 85.21 -0.87 -0.49 -0.37 -0.78 -0.48 -0.31 PSI 47
48 GS−MetaServer2 78.42 64.91 82.61 82.50 75.09 83.12 -0.71 -1.69 -0.30 -0.63 -0.72 -0.36 79.74 75.88 84.51 84.17 80.09 84.93 -0.87 -0.63 -0.30 -0.70 -0.57 -0.38 GS−MetaServer2 48
49 mariner1 78.42 61.49 85.92 82.22 79.26 86.21 -0.71 -2.20 0.40 -0.69 -0.11 0.32 81.05 75.70 85.93 83.61 79.91 86.45 -0.52 -0.66 0.07 -0.86 -0.61 0.03 mariner1 49
50 COMA 78.16 75.88 83.52 81.94 79.54 84.10 -0.77 -0.04 -0.11 -0.76 -0.07 -0.14 78.16 75.88 83.52 81.94 79.54 84.10 -1.29 -0.63 -0.56 -1.31 -0.68 -0.61 COMA 50
51 3D−JIGSAW_AEP 78.16 75.88 80.88 82.22 79.81 81.33 -0.77 -0.04 -0.67 -0.69 -0.03 -0.75 78.16 75.88 80.98 82.22 79.81 81.44 -1.29 -0.63 -1.23 -1.23 -0.63 -1.33 3D−JIGSAW_AEP 51
52 panther_server 77.63 70.44 79.36 81.67 74.07 79.68 -0.89 -0.86 -0.99 -0.82 -0.87 -1.11 77.63 73.25 79.36 81.67 75.74 79.68 -1.43 -1.13 -1.65 -1.38 -1.39 -1.80 panther_server 52
53 SAM−T06−server 77.11 66.58 76.08 79.72 71.20 76.58 -1.01 -1.44 -1.68 -1.27 -1.30 -1.78 77.11 70.88 78.38 79.72 74.17 79.99 -1.57 -1.58 -1.91 -1.91 -1.69 -1.72 SAM−T06−server 53
54 GeneSilicoMetaServer 76.84 74.39 82.33 79.72 72.87 82.60 -1.08 -0.26 -0.36 -1.27 -1.05 -0.47 84.21 83.51 87.30 88.89 88.15 88.95 0.32 0.83 0.43 0.58 0.95 0.70 GeneSilicoMetaServer 54
55 nFOLD3 76.84 71.58 77.92 80.83 75.28 78.99 -1.08 -0.69 -1.30 -1.02 -0.70 -1.26 80.53 75.26 81.82 84.17 79.17 82.57 -0.66 -0.74 -1.01 -0.70 -0.75 -1.02 nFOLD3 55
56 3DShot2 76.32 70.35 77.43 79.44 65.93 77.75 -1.20 -0.87 -1.40 -1.34 -2.07 -1.53 76.32 70.35 77.43 79.44 65.93 77.75 -1.78 -1.68 -2.15 -1.99 -3.25 -2.32 3DShot2 56
57 circle 73.68 66.49 74.21 76.39 69.17 74.21 -1.81 -1.45 -2.08 -2.04 -1.60 -2.30 86.84 84.39 87.97 90.00 89.26 88.43 1.02 0.99 0.60 0.88 1.16 0.56 circle 57
58 SAM−T02−server 73.16 68.60 71.20 77.22 72.41 72.79 -1.93 -1.13 -2.72 -1.85 -1.12 -2.61 73.16 68.60 72.84 77.22 72.41 74.01 -2.63 -2.01 -3.35 -2.59 -2.02 -3.33 SAM−T02−server 58
59 FFASstandard 73.16 64.21 75.87 77.22 67.78 77.48 -1.93 -1.79 -1.73 -1.85 -1.80 -1.59 83.95 83.60 86.09 88.61 88.24 87.74 0.25 0.84 0.11 0.50 0.97 0.37 FFASstandard 59
60 3Dpro 72.63 64.39 76.24 75.56 66.85 76.62 -2.06 -1.77 -1.65 -2.24 -1.94 -1.78 72.63 68.51 76.24 75.56 72.04 76.62 -2.77 -2.03 -2.47 -3.04 -2.09 -2.63 3Dpro 60
61 FFASflextemplate 72.63 63.86 75.25 76.67 67.41 76.85 -2.06 -1.85 -1.86 -1.98 -1.86 -1.73 73.68 68.60 75.57 77.78 72.41 77.18 -2.49 -2.01 -2.64 -2.44 -2.02 -2.47 FFASflextemplate 61
62 OLGAFS 72.11 66.32 73.73 76.11 70.00 75.33 -2.18 -1.48 -2.18 -2.11 -1.47 -2.06 77.63 66.32 83.06 81.39 78.43 83.61 -1.43 -2.45 -0.68 -1.46 -0.89 -0.74 OLGAFS 62
63 FFASsuboptimal 72.11 66.14 74.43 76.11 69.81 76.02 -2.18 -1.50 -2.03 -2.11 -1.50 -1.91 72.63 67.02 75.69 76.67 70.74 77.29 -2.77 -2.31 -2.61 -2.74 -2.34 -2.45 FFASsuboptimal 63
64 rehtnap 69.47 62.10 67.08 73.06 64.54 68.38 -2.79 -2.11 -3.59 -2.81 -2.28 -3.57 69.47 62.10 67.08 73.06 65.00 68.38 -3.61 -3.25 -4.86 -3.72 -3.42 -4.85 rehtnap 64
65 FUGUE_KM 68.95 62.81 69.75 72.78 66.30 71.33 -2.91 -2.01 -3.02 -2.88 -2.02 -2.93 81.58 73.86 82.27 86.11 77.96 83.91 -0.38 -1.01 -0.89 -0.18 -0.97 -0.66 FUGUE_KM 65
66 FOLDpro 61.05 54.74 59.84 64.44 57.78 59.84 -4.75 -3.22 -5.12 -4.81 -3.27 -5.44 71.84 68.51 70.66 75.56 72.04 71.04 -2.98 -2.03 -3.93 -3.04 -2.09 -4.13 FOLDpro 66
67 MUFOLD−MD 53.95 38.77 65.44 56.67 40.65 65.75 -6.40 -5.62 -3.93 -6.61 -5.79 -4.15 68.68 58.95 70.09 71.67 61.39 70.55 -3.82 -3.85 -4.07 -4.10 -4.11 -4.26 MUFOLD−MD 67
68 FALCON_CONSENSUS 50.53 37.10 57.42 53.33 39.17 57.79 -7.20 -5.87 -5.63 -7.38 -6.01 -5.88 50.53 44.56 57.42 53.33 46.76 57.79 -8.66 -6.59 -7.39 -9.07 -6.87 -7.70 FALCON_CONSENSUS 68
69 schenk−torda−server 20.26 16.58 25.57 21.39 17.50 26.12 -14.24 -8.96 -12.36 -14.78 -9.20 -12.79 22.11 18.68 29.18 23.33 19.72 29.06 -16.24 -11.51 -14.78 -17.22 -11.98 -15.45 schenk−torda−server 69
70 RANDOM 19.31 15.55 19.31 20.88 17.09 20.88 -14.46 -9.12 -13.69 -14.90 -9.26 -13.93 19.31 15.55 19.31 20.88 17.09 20.88 -16.98 -12.11 -17.36 -17.88 -12.48 -17.66 RANDOM 70
71 mahmood−torda−server 16.32 12.81 22.65 16.11 12.78 22.70 -15.15 -9.53 -12.98 -16.00 -9.90 -13.53 20.26 16.40 28.97 21.39 17.32 29.31 -16.73 -11.95 -14.83 -17.74 -12.43 -15.39 mahmood−torda−server 71
72 BHAGEERATH                                     -14.46 -9.12 -13.69 -14.90 -9.26 -13.93                                     -16.98 -12.11 -17.36 -17.88 -12.48 -17.66 BHAGEERATH 72
73 Fiser−M4T                                     -14.46 -9.12 -13.69 -14.90 -9.26 -13.93                                     -16.98 -12.11 -17.36 -17.88 -12.48 -17.66 Fiser−M4T 73
74 test_http_server_01                                     -14.46 -9.12 -13.69 -14.90 -9.26 -13.93                                     -16.98 -12.11 -17.36 -17.88 -12.48 -17.66 test_http_server_01 74