T0390

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

T0390

ephrin A1 Homo sapiens

Target type: Server only

Target sequence:

>T0390 EFNA1A, Homo sapiens, 182 residues
AAPEHHHHHHDYDIPTTENLYFQGAMDAADRHTVFWNSSNPKFRNEDYTIHVQLNDYVDIICPHYEDHSVADAAMEQYILYLVEHEEYQLCQPQSKDQVRWQCNRPSAKHGPEKLSEKFQRFTPFTLGKEFKEGHSYYYISKPIHQHEDRCLRLKVTVSGKITHSPQAHVNPQEKRLAADDP

Structure:
Method: X-ray, res=2.65Å, R/Rfree=0.20/0.23
Determined by: SGC
PDB ID: 3czu

3czu_B
Ribbon diagram of 390: 3czu chain B

PyMOL of 3czu

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

Cupredoxin-like fold. Lacks the metal-binding site of cupredoxins, but is homologous to them.

3czu_B cartoon
Cartoon diagram of 390: chain B

CASP category:

Comparative modeling:easy.

Closest templates:

1shw

Target sequence - PDB file inconsistencies:

28 N-terminal residues 1-AAPEHHHHHHDYDIPTTENLYFQGAMDA-28, 2 internal residues 67-DH-68 and 23 C-terminal residues 161-KITHSPQAHVNPQEKRLAADDP-182 of the target sequence are missing from PDB coordinates. Residue 18 in PDB corresponds to residue 29 in the target sequence.

T0390    3czu.pdb    T0390.pdb    PyMOL    PyMOL of domains    

T0390    1 AAPEHHHHHHDYDIPTTENLYFQGAMDAADRHTVFWNSSNPKFRNEDYTIHVQLNDYVDIICPHYEDHSVADAAMEQYILYLVEHEEYQLCQPQSKDQVRWQCNRPSAKHGPEKLSEKFQRFTPFTLGKEFKEGHSYYYISKPIHQHEDRCLRLKVTVSGKITHSPQAHVNPQEKRLAADDP 182
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~||||||||||||||||||||||||||||||||||||||~~||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~~~~~~~~~~~~~~~~~~~
3czuA   18 ----------------------------ADRHTVFWNSSNPKFRNEDYTIHVQLNDYVDIICPHYE--SVADAAMEQYILYLVEHEEYQLCQPQSKDQVRWQCNRPSAKHGPEKLSEKFQRFTPFTLGKEFKEGHSYYYISKPIHQHEDRCLRLKVTVSG---------------------- 149

Single domain protein: target 29-66, 69-160 ; pdb 18-55, 58-149

Sequence classification:

Eprin family (PF00812) in Pfam.

Server predictions:

T0390:pdb 18-149:seq 29-160:CM_easy;   alignment

distribution of first scores
First models for T0390: 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 #
T0390 T0390 T0390 T0390
First score First Z-score Best score Best Z-score
1 MULTICOM−REFINE 89.61 87.56 90.82 0.74 0.92 0.56 89.61 87.56 91.30 0.65 0.82 0.52 MULTICOM−REFINE 1
2 MULTICOM−CLUSTER 89.61 87.31 91.07 0.74 0.88 0.58 89.61 87.31 91.07 0.65 0.78 0.49 MULTICOM−CLUSTER 2
3 MUSTER 89.61 84.42 90.75 0.74 0.43 0.55 89.61 86.22 91.28 0.65 0.57 0.51 MUSTER 3
4 nFOLD3 89.42 86.86 90.76 0.70 0.81 0.55 89.42 86.86 90.76 0.61 0.69 0.45 nFOLD3 4
5 MULTICOM−CMFR 89.42 86.73 90.71 0.70 0.79 0.55 89.81 86.73 91.70 0.69 0.67 0.57 MULTICOM−CMFR 5
6 Pcons_local 89.23 86.54 90.70 0.67 0.76 0.54 89.23 86.54 90.70 0.57 0.63 0.44 Pcons_local 6
7 Pcons_dot_net 89.23 86.54 90.70 0.67 0.76 0.54 89.23 86.80 90.70 0.57 0.68 0.44 Pcons_dot_net 7
8 Pcons_multi 89.23 86.54 90.70 0.67 0.76 0.54 89.61 87.18 91.34 0.65 0.75 0.52 Pcons_multi 8
9 MUProt 89.04 86.86 90.99 0.64 0.81 0.57 90.00 88.20 91.63 0.73 0.95 0.56 MUProt 9
10 PS2−server 89.04 86.60 90.89 0.64 0.77 0.56 89.04 86.60 90.89 0.53 0.64 0.46 PS2−server 10
11 3DShot2 89.04 86.22 90.76 0.64 0.71 0.55 89.04 86.22 90.76 0.53 0.57 0.45 3DShot2 11
12 BAKER−ROBETTA 88.85 86.67 90.76 0.61 0.78 0.55 89.23 87.44 90.76 0.57 0.80 0.45 BAKER−ROBETTA 12
13 PSI 88.85 86.41 90.75 0.61 0.74 0.55 88.85 86.41 90.75 0.49 0.60 0.44 PSI 13
14 GeneSilicoMetaServer 88.85 84.36 90.52 0.61 0.42 0.53 88.85 85.39 90.52 0.49 0.41 0.41 GeneSilicoMetaServer 14
15 FOLDpro 88.65 86.47 91.37 0.58 0.75 0.61 88.65 86.47 91.37 0.45 0.62 0.53 FOLDpro 15
16 keasar−server 88.65 84.94 90.72 0.58 0.51 0.55 88.85 85.39 90.72 0.49 0.41 0.44 keasar−server 16
17 HHpred2 88.46 86.15 90.66 0.55 0.70 0.54 88.46 86.15 90.66 0.41 0.56 0.43 HHpred2 17
18 FAMSD 88.46 85.64 90.04 0.55 0.62 0.48 88.46 85.64 90.04 0.41 0.46 0.35 FAMSD 18
19 pro−sp3−TASSER 88.27 85.58 89.59 0.51 0.61 0.43 88.27 85.58 89.59 0.37 0.45 0.29 pro−sp3−TASSER 19
20 RAPTOR 88.27 85.58 90.67 0.51 0.61 0.54 88.27 85.58 90.67 0.37 0.45 0.43 RAPTOR 20
21 LEE−SERVER 88.27 84.94 90.41 0.51 0.51 0.51 89.23 87.05 91.57 0.57 0.73 0.55 LEE−SERVER 21
22 MULTICOM−RANK 88.08 85.51 90.70 0.48 0.60 0.54 89.23 85.51 91.55 0.57 0.43 0.55 MULTICOM−RANK 22
23 Zhang−Server 88.08 85.00 90.54 0.48 0.52 0.53 88.85 85.64 90.69 0.49 0.46 0.44 Zhang−Server 23
24 fais−server 88.08 84.74 90.74 0.48 0.48 0.55 89.04 87.11 90.74 0.53 0.74 0.44 fais−server 24
25 circle 88.08 84.74 89.72 0.48 0.48 0.44 88.08 85.51 89.77 0.33 0.43 0.32 circle 25
26 FFASflextemplate 88.08 84.23 90.68 0.48 0.40 0.54 88.08 84.23 90.68 0.33 0.19 0.44 FFASflextemplate 26
27 FFASsuboptimal 88.08 82.44 89.09 0.48 0.12 0.38 89.61 87.82 91.04 0.65 0.87 0.48 FFASsuboptimal 27
28 3Dpro 87.89 85.32 91.32 0.45 0.57 0.61 88.65 86.47 91.37 0.45 0.62 0.53 3Dpro 28
29 mGenTHREADER 87.89 84.42 89.55 0.45 0.43 0.43 87.89 84.42 89.55 0.29 0.22 0.29 mGenTHREADER 29
30 GS−KudlatyPred 87.69 85.13 90.75 0.42 0.54 0.55 87.69 85.13 90.75 0.25 0.36 0.44 GS−KudlatyPred 30
31 FFASstandard 87.69 83.20 90.68 0.42 0.24 0.54 88.08 84.23 90.68 0.33 0.19 0.44 FFASstandard 31
32 Frankenstein 87.69 81.92 89.22 0.42 0.04 0.39 87.69 81.92 89.22 0.25 -0.25 0.25 Frankenstein 32
33 Poing 87.50 83.40 90.91 0.39 0.27 0.57 87.50 83.40 90.91 0.21 0.03 0.47 Poing 33
34 Phyre2 87.50 83.40 90.91 0.39 0.27 0.57 87.50 83.40 90.91 0.21 0.03 0.47 Phyre2 34
35 Phyre_de_novo 87.50 83.40 90.91 0.39 0.27 0.57 87.50 83.40 90.91 0.21 0.03 0.47 Phyre_de_novo 35
36 Phragment 87.50 83.40 90.91 0.39 0.27 0.57 87.50 83.40 90.91 0.21 0.03 0.47 Phragment 36
37 Pushchino 87.31 85.26 88.34 0.36 0.56 0.30 87.31 85.26 88.34 0.17 0.39 0.13 Pushchino 37
38 BioSerf 87.11 83.40 89.79 0.32 0.27 0.45 87.11 83.40 89.79 0.13 0.03 0.32 BioSerf 38
39 pipe_int 87.11 83.14 89.83 0.32 0.23 0.45 87.31 83.14 90.51 0.17 -0.02 0.41 pipe_int 39
40 GS−MetaServer2 86.92 83.97 90.02 0.29 0.36 0.47 86.92 83.97 90.02 0.09 0.14 0.35 GS−MetaServer2 40
41 HHpred4 86.73 82.24 89.82 0.26 0.09 0.45 86.73 82.24 89.82 0.05 -0.19 0.32 HHpred4 41
42 HHpred5 86.73 82.24 89.82 0.26 0.09 0.45 86.73 82.24 89.82 0.05 -0.19 0.32 HHpred5 42
43 Fiser−M4T 86.54 82.56 88.95 0.23 0.14 0.36 86.54 82.56 88.95 0.01 -0.13 0.21 Fiser−M4T 43
44 SAM−T08−server 86.15 83.46 88.12 0.17 0.28 0.28 87.31 83.46 89.16 0.17 0.04 0.24 SAM−T08−server 44
45 panther_server 85.96 83.01 86.35 0.13 0.21 0.09 85.96 83.01 86.35 -0.11 -0.04 -0.13 panther_server 45
46 YASARA 85.96 82.89 89.13 0.13 0.19 0.38 86.15 83.97 89.13 -0.07 0.14 0.23 YASARA 46
47 forecast 85.77 81.15 87.74 0.10 -0.08 0.24 85.77 81.15 87.74 -0.15 -0.40 0.05 forecast 47
48 CpHModels 85.39 82.31 84.55 0.04 0.10 -0.09 85.39 82.31 84.55 -0.23 -0.18 -0.36 CpHModels 48
49 3D−JIGSAW_V3 84.81 81.60 84.83 -0.06 -0.01 -0.06 87.89 85.19 90.48 0.29 0.37 0.41 3D−JIGSAW_V3 49
50 SAM−T02−server 84.23 80.13 80.64 -0.15 -0.24 -0.50 84.23 80.13 80.64 -0.47 -0.60 -0.87 SAM−T02−server 50
51 SAM−T06−server 82.50 78.78 83.75 -0.44 -0.45 -0.17 82.50 79.68 83.75 -0.83 -0.68 -0.47 SAM−T06−server 51
52 METATASSER 82.50 74.87 81.19 -0.44 -1.06 -0.44 84.04 81.03 83.29 -0.51 -0.42 -0.53 METATASSER 52
53 huber−torda−server 82.31 78.97 80.62 -0.47 -0.42 -0.50 82.31 78.97 80.62 -0.87 -0.82 -0.88 huber−torda−server 53
54 COMA 81.92 76.54 77.76 -0.53 -0.80 -0.79 81.92 76.54 77.76 -0.95 -1.28 -1.25 COMA 54
55 Distill 80.00 74.74 73.53 -0.85 -1.08 -1.23 81.15 74.74 76.26 -1.11 -1.63 -1.44 Distill 55
56 COMA−M 79.23 76.80 73.06 -0.97 -0.76 -1.28 79.23 76.80 73.06 -1.51 -1.23 -1.86 COMA−M 56
57 ACOMPMOD 72.50 68.14 63.11 -2.08 -2.11 -2.31 72.50 68.14 63.11 -2.90 -2.89 -3.16 ACOMPMOD 57
58 FALCON_CONSENSUS 71.73 69.55 60.88 -2.21 -1.89 -2.54 88.85 86.41 90.75 0.49 0.60 0.44 FALCON_CONSENSUS 58
59 FALCON 71.73 69.55 60.88 -2.21 -1.89 -2.54 88.85 86.41 90.75 0.49 0.60 0.44 FALCON 59
60 FUGUE_KM 71.54 69.36 60.51 -2.24 -1.92 -2.58 71.54 69.36 60.51 -3.10 -2.65 -3.50 FUGUE_KM 60
61 3D−JIGSAW_AEP 70.58 66.35 62.99 -2.40 -2.39 -2.32 87.11 83.40 89.92 0.13 0.03 0.34 3D−JIGSAW_AEP 61
62 FEIG 69.42 63.65 71.85 -2.59 -2.81 -1.41 85.00 81.03 81.18 -0.31 -0.42 -0.80 FEIG 62
63 rehtnap 60.58 55.96 49.65 -4.05 -4.01 -3.70 60.77 55.96 50.16 -5.34 -5.21 -4.85 rehtnap 63
64 mariner1 35.00 25.58 36.28 -8.26 -8.76 -5.09 49.42 38.78 51.96 -7.70 -8.50 -4.61 mariner1 64
65 MUFOLD−MD 20.77 19.49 25.97 -10.60 -9.71 -6.15 20.77 19.49 25.97 -13.66 -12.18 -8.00 MUFOLD−MD 65
66 MUFOLD−Server 19.04 16.80 18.18 -10.89 -10.13 -6.96 19.04 16.80 18.19 -14.01 -12.70 -9.01 MUFOLD−Server 66
67 RBO−Proteus 17.69 15.83 21.56 -11.11 -10.28 -6.61 18.85 17.69 25.44 -14.05 -12.53 -8.07 RBO−Proteus 67
68 RANDOM 15.07 12.36 15.07 -11.54 -10.82 -7.28 15.07 12.36 15.07 -14.84 -13.55 -9.42 RANDOM 68
69 schenk−torda−server 12.69 12.12 14.72 -11.93 -10.86 -7.32 15.58 13.21 14.90 -14.73 -13.38 -9.44 schenk−torda−server 69
70 OLGAFS 12.12 10.00 9.07 -12.03 -11.19 -7.90 12.50 10.26 11.30 -15.37 -13.95 -9.91 OLGAFS 70
71 mahmood−torda−server 11.35 9.55 16.40 -12.15 -11.26 -7.14 12.88 11.35 17.63 -15.29 -13.74 -9.09 mahmood−torda−server 71
72 BHAGEERATH                   -11.54 -10.82 -7.28                   -14.84 -13.55 -9.42 BHAGEERATH 72
73 LOOPP_Server                   -11.54 -10.82 -7.28                   -14.84 -13.55 -9.42 LOOPP_Server 73
74 test_http_server_01                   -11.54 -10.82 -7.28                   -14.84 -13.55 -9.42 test_http_server_01 74