T0402

X-ray Targets
387 388 389 390
391 392 393 394
395 396 397 398
399 400 401 402
403 404 405 406
407 408 409 410
411 412 413 414
415 416 417 418
419 420 421 422
423 424 425 426
427 428 429 430
431 432 433 434
435 436 438 439
440 441 442 443
444 445 446 447
448 449 450 451
452 453 454 455
456 457 458 459
461 463 465 470
477 478 479 481
483 485 486 487
488 489 490 491
493 494 495 496
497 501 502 503
504 505 506 507
508 509 510 511
512 513 514

T0402

putative pyridoxamine 5'-phosphate oxidase (NP_472219.1) from Listeria innocua

Target type: Server only

Target sequence:

>T0402 NP_472219.1, LISTERIA INNOCUA, 139 residues
MENELEDKILAILEQHQVGVLTSVQGDFPHARYMTFLHDGLTLYTPSGKELPKTEEVRRNPHVCVLIGYDSPGSAFLEINGLASLEEDESIKERIWENISKDWFQGEDSPSFVVIKIVPEQIRILNSDDDGPDTLDLIG

Structure:
Method: X-ray, res=2.0Å, R/Rfree=0.19/0.24
Determined by: JCSG
PDB ID: 3db0

3db0_A cartoon
Cartoon diagram of 402: 3db0 chain A

PyMOL of 3db0

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Split β-barrel fold.

CASP category:

Comparative modeling:medium.

Closest templates:

2qea.

Target sequence - PDB file inconsistencies:

T0402    3db0.pdb    T0402.pdb    PyMOL    PyMOL of domains    

T0402    1 MENELEDKILAILEQHQVGVLTSVQGDFPHARYMTFLHDGLTLYTPSGKELPKTEEVRRNPHVCVLIGYDSPGSAFLEINGLASLEEDESIKERIWENISKDWFQGEDSPSFVVIKIVPEQIRILNSDDDGPDTLDLIG 139
           |||||||||||||||||||||||||||||||||||||||||||||||~~~~||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~|||||||||||||||~~~~~~~~~~~~~
3db0A    1 MENELEDKILAILEQHQVGVLTSVQGDFPHARYMTFLHDGLTLYTPS----PKTEEVRRNPHVCVLIGYDSPGSAFLEINGLASLEEDESIKERIWENISKDWFQ------FVVIKIVPEQIRILN------------- 126

Residue change log: change 1, 34, MSE to MET;

Single domain protein: target 1-47, 52-105, 112-126 ; pdb 1-47, 52-105, 112-126

Sequence classification:

Pyridoxamine 5'-phosphate oxidase (Pyridox_oxidase) in Pfam.

Server predictions:

T0402:pdb 1-126:seq 1-126:CM_medium;   alignment

distribution of first scores
First models for T0402: 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 #
T0402 T0402 T0402 T0402
First score First Z-score Best score Best Z-score
1 Phyre_de_novo 79.53 75.36 85.23 2.02 2.27 1.38 79.53 75.36 85.23 2.28 2.16 1.32 Phyre_de_novo 1
2 pro−sp3−TASSER 79.31 74.14 83.98 1.97 2.01 1.14 79.31 76.65 83.98 2.21 2.47 1.03 pro−sp3−TASSER 2
3 Zhang−Server 76.51 70.19 85.96 1.32 1.19 1.53 77.37 72.34 86.20 1.58 1.44 1.54 Zhang−Server 3
4 MULTICOM−CLUSTER 76.29 70.26 83.05 1.27 1.21 0.96 76.29 70.26 83.05 1.23 0.94 0.82 MULTICOM−CLUSTER 4
5 3D−JIGSAW_AEP 75.86 72.99 79.91 1.17 1.77 0.36 75.86 72.99 79.91 1.09 1.60 0.10 3D−JIGSAW_AEP 5
6 LEE−SERVER 75.86 70.55 73.71 1.17 1.27 -0.84 76.08 73.49 73.71 1.16 1.72 -1.32 LEE−SERVER 6
7 METATASSER 75.86 69.68 81.48 1.17 1.08 0.66 78.23 75.79 83.38 1.86 2.27 0.90 METATASSER 7
8 HHpred2 75.22 69.04 81.58 1.02 0.95 0.68 75.22 69.04 81.58 0.88 0.65 0.48 HHpred2 8
9 rehtnap 75.00 69.83 79.14 0.97 1.12 0.21 75.00 69.83 79.14 0.81 0.84 -0.08 rehtnap 9
10 Pcons_multi 75.00 69.68 80.99 0.97 1.08 0.57 75.43 69.68 81.03 0.95 0.81 0.36 Pcons_multi 10
11 3D−JIGSAW_V3 74.57 68.53 82.63 0.87 0.84 0.88 74.57 68.61 82.67 0.67 0.55 0.73 3D−JIGSAW_V3 11
12 SAM−T08−server 74.57 66.81 81.74 0.87 0.49 0.71 74.57 66.81 81.74 0.67 0.12 0.52 SAM−T08−server 12
13 COMA−M 74.35 69.33 82.81 0.81 1.01 0.92 76.29 71.84 82.81 1.23 1.32 0.77 COMA−M 13
14 FEIG 74.35 68.03 81.69 0.81 0.74 0.70 75.65 70.19 81.69 1.02 0.93 0.51 FEIG 14
15 SAM−T02−server 73.92 68.75 79.26 0.71 0.89 0.23 73.92 68.75 79.26 0.46 0.58 -0.05 SAM−T02−server 15
16 fais−server 73.92 68.32 78.78 0.71 0.80 0.14 73.92 68.32 81.03 0.46 0.48 0.36 fais−server 16
17 GS−KudlatyPred 73.92 67.31 81.22 0.71 0.59 0.61 73.92 67.31 81.22 0.46 0.24 0.40 GS−KudlatyPred 17
18 pipe_int 73.92 67.17 80.92 0.71 0.56 0.55 73.92 68.32 83.81 0.46 0.48 1.00 pipe_int 18
19 Frankenstein 73.71 68.53 82.48 0.66 0.84 0.85 74.14 68.53 82.48 0.53 0.53 0.69 Frankenstein 19
20 COMA 73.71 67.39 79.67 0.66 0.61 0.31 74.14 67.39 82.81 0.53 0.26 0.77 COMA 20
21 FFASstandard 73.71 65.81 83.22 0.66 0.28 1.00 73.71 68.17 83.22 0.39 0.44 0.86 FFASstandard 21
22 FFASflextemplate 73.49 67.74 81.50 0.61 0.68 0.66 73.71 67.74 81.50 0.39 0.34 0.47 FFASflextemplate 22
23 FALCON_CONSENSUS 73.49 67.31 81.89 0.61 0.59 0.74 73.49 67.31 81.91 0.32 0.24 0.56 FALCON_CONSENSUS 23
24 FALCON 73.49 67.31 81.89 0.61 0.59 0.74 75.43 70.26 82.84 0.95 0.94 0.77 FALCON 24
25 Pcons_local 73.49 66.88 79.43 0.61 0.50 0.26 74.35 70.19 79.43 0.60 0.93 -0.01 Pcons_local 25
26 Pcons_dot_net 73.49 66.88 79.43 0.61 0.50 0.26 74.35 70.19 79.80 0.60 0.93 0.08 Pcons_dot_net 26
27 panther_server 73.49 66.31 79.33 0.61 0.38 0.24 73.49 66.31 79.33 0.32 0.00 -0.03 panther_server 27
28 keasar−server 73.06 66.02 81.08 0.51 0.32 0.58 74.14 69.40 81.50 0.53 0.74 0.47 keasar−server 28
29 SAM−T06−server 72.63 65.88 81.35 0.41 0.29 0.63 72.63 66.02 81.35 0.04 -0.07 0.43 SAM−T06−server 29
30 PS2−server 72.63 65.73 81.56 0.41 0.26 0.68 72.63 65.73 83.33 0.04 -0.14 0.89 PS2−server 30
31 FFASsuboptimal 72.41 67.53 81.38 0.36 0.64 0.64 72.63 67.96 82.59 0.04 0.39 0.72 FFASsuboptimal 31
32 mGenTHREADER 72.41 66.81 79.88 0.36 0.49 0.35 72.41 66.81 79.88 -0.04 0.12 0.09 mGenTHREADER 32
33 RAPTOR 72.41 66.38 80.58 0.36 0.40 0.49 72.41 66.38 84.64 -0.04 0.02 1.19 RAPTOR 33
34 BioSerf 72.20 65.44 82.14 0.31 0.20 0.79 72.20 65.44 82.14 -0.10 -0.21 0.61 BioSerf 34
35 GS−MetaServer2 71.98 63.22 78.84 0.26 -0.26 0.15 73.71 67.31 81.81 0.39 0.24 0.54 GS−MetaServer2 35
36 PSI 71.34 65.16 80.95 0.11 0.14 0.56 72.20 65.16 81.96 -0.10 -0.27 0.57 PSI 36
37 BAKER−ROBETTA 70.91 64.58 77.98 0.01 0.02 -0.02 73.06 67.17 80.67 0.18 0.21 0.28 BAKER−ROBETTA 37
38 3DShot2 70.91 64.01 73.02 0.01 -0.10 -0.97 70.91 64.01 73.02 -0.53 -0.55 -1.48 3DShot2 38
39 Fiser−M4T 70.91 61.42 78.14 0.01 -0.64 0.01 70.91 61.42 78.14 -0.53 -1.17 -0.30 Fiser−M4T 39
40 MULTICOM−REFINE 70.04 63.15 73.51 -0.19 -0.28 -0.88 70.04 63.65 73.51 -0.81 -0.64 -1.37 MULTICOM−REFINE 40
41 3Dpro 69.83 59.91 77.20 -0.24 -0.95 -0.17 69.83 59.91 77.20 -0.88 -1.53 -0.52 3Dpro 41
42 MUProt 69.61 62.86 72.93 -0.29 -0.34 -0.99 69.83 64.80 73.16 -0.88 -0.36 -1.45 MUProt 42
43 HHpred4 69.40 61.35 81.59 -0.34 -0.65 0.68 69.40 61.35 81.59 -1.02 -1.19 0.49 HHpred4 43
44 HHpred5 68.97 61.78 69.02 -0.44 -0.56 -1.75 68.97 61.78 69.02 -1.16 -1.08 -2.40 HHpred5 44
45 CpHModels 68.32 61.85 71.65 -0.59 -0.55 -1.24 68.32 61.85 71.65 -1.37 -1.07 -1.79 CpHModels 45
46 forecast 68.32 58.69 78.31 -0.59 -1.20 0.05 68.32 58.69 78.31 -1.37 -1.82 -0.27 forecast 46
47 MULTICOM−CMFR 68.10 64.66 69.32 -0.65 0.04 -1.69 70.47 65.09 72.64 -0.67 -0.29 -1.57 MULTICOM−CMFR 47
48 YASARA 68.10 61.92 79.80 -0.65 -0.53 0.34 75.86 68.82 83.90 1.09 0.60 1.02 YASARA 48
49 MULTICOM−RANK 67.89 63.58 78.25 -0.69 -0.19 0.04 67.89 63.58 78.35 -1.51 -0.65 -0.26 MULTICOM−RANK 49
50 MUSTER 67.24 61.64 71.58 -0.85 -0.59 -1.25 71.55 64.51 79.96 -0.32 -0.43 0.11 MUSTER 50
51 Phragment 66.38 57.33 76.64 -1.05 -1.49 -0.28 70.47 63.36 76.64 -0.67 -0.71 -0.65 Phragment 51
52 Poing 66.16 57.11 76.62 -1.10 -1.53 -0.28 70.47 63.36 76.62 -0.67 -0.71 -0.65 Poing 52
53 Phyre2 66.16 57.11 76.80 -1.10 -1.53 -0.24 70.47 63.36 76.80 -0.67 -0.71 -0.61 Phyre2 53
54 FAMSD 65.30 60.13 80.80 -1.30 -0.90 0.53 73.49 67.46 84.73 0.32 0.28 1.21 FAMSD 54
55 nFOLD3 65.09 62.00 74.62 -1.35 -0.52 -0.67 69.40 64.51 80.27 -1.02 -0.43 0.18 nFOLD3 55
56 LOOPP_Server 64.87 57.83 78.40 -1.40 -1.38 0.06 68.75 63.43 80.33 -1.23 -0.69 0.20 LOOPP_Server 56
57 circle 64.66 59.91 79.21 -1.45 -0.95 0.22 72.84 62.36 81.04 0.10 -0.94 0.36 circle 57
58 FOLDpro 64.22 58.19 70.17 -1.55 -1.31 -1.53 69.83 59.91 77.20 -0.88 -1.53 -0.52 FOLDpro 58
59 ACOMPMOD 63.58 58.26 77.00 -1.70 -1.29 -0.21 69.83 61.06 78.17 -0.88 -1.25 -0.30 ACOMPMOD 59
60 FUGUE_KM 63.15 59.12 74.01 -1.80 -1.11 -0.78 68.97 61.92 74.01 -1.16 -1.05 -1.25 FUGUE_KM 60
61 MUFOLD−Server 62.50 55.32 60.31 -1.95 -1.91 -3.43 62.50 55.32 60.36 -3.27 -2.63 -4.38 MUFOLD−Server 61
62 GeneSilicoMetaServer 62.07 58.76 71.12 -2.05 -1.19 -1.34 72.20 67.31 79.01 -0.10 0.24 -0.11 GeneSilicoMetaServer 62
63 Distill 59.27 47.92 57.34 -2.71 -3.45 -4.01 60.34 53.45 59.13 -3.97 -3.07 -4.66 Distill 63
64 Pushchino 54.09 46.48 55.09 -3.92 -3.75 -4.44 54.09 46.48 55.09 -6.01 -4.74 -5.59 Pushchino 64
65 RBO−Proteus 26.51 23.78 44.43 -10.35 -8.48 -6.50 26.51 23.92 44.43 -14.99 -10.13 -8.04 RBO−Proteus 65
66 MUFOLD−MD 20.91 17.17 42.08 -11.66 -9.85 -6.95 22.63 19.61 44.41 -16.26 -11.16 -8.04 MUFOLD−MD 66
67 mariner1 18.97 15.88 17.54 -12.11 -10.12 -11.70 64.44 55.96 73.06 -2.63 -2.47 -1.47 mariner1 67
68 schenk−torda−server 16.16 13.15 20.81 -12.77 -10.69 -11.06 16.16 13.79 24.52 -18.37 -12.56 -12.60 schenk−torda−server 68
69 RANDOM 16.13 13.94 16.13 -12.78 -10.52 -11.97 16.13 13.94 16.13 -18.38 -12.52 -14.53 RANDOM 69
70 OLGAFS 15.30 12.57 11.20 -12.97 -10.81 -12.92 15.30 12.57 11.50 -18.65 -12.85 -15.59 OLGAFS 70
71 mahmood−torda−server 13.36 9.05 23.37 -13.42 -11.54 -10.57 17.46 15.73 24.11 -17.94 -12.09 -12.70 mahmood−torda−server 71
72 BHAGEERATH                   -12.78 -10.52 -11.97                   -18.38 -12.52 -14.53 BHAGEERATH 72
73 huber−torda−server                   -12.78 -10.52 -11.97                   -18.38 -12.52 -14.53 huber−torda−server 73
74 test_http_server_01                   -12.78 -10.52 -11.97                   -18.38 -12.52 -14.53 test_http_server_01 74