Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr7 43982449 . T A CCDS5474.1:NM_015983.3:c.113aTg>aAg_NP_057067.1:p.38M>K Homo sapiens ubiquitin conjugating enzyme E2 D4 (putative) (UBE2D4), mRNA.
pdb_id: 
label_asym_id: 
label_seq_id: 
label_comp_id: 
auth_asym_id: 
auth_seq_id: 
alphafold_id: 
label_asym_id: 
label_seq_id: 
label_comp_id: 
auth_asym_id: 
auth_seq_id: 

PDB

Entity Residue Monomer BioUnit Ligand View
PDB Entity Uniprot Identity Evalue ExpMethod Date Name Label Auth ASA rASA SS φ ψ ASA rASA ΔASA Interaction Name Distance Atom(p) Atom(l)
2oxq 1 Q6PC58 95.92 5e-106 X-RAY
 2008-02-19 MET A:43 A:38 74.0 0.4 E -90.5 137.7 74.0 0.4 0.0
MET B:43 B:38 79.0 0.427 E -90.2 119.5 79.0 0.427 0.0
3tgd 1 P62837 93.2 6e-104 X-RAY
 2011-08-31 MET A:43 A:38 84.0 0.454 E -85.4 134.8 84.0 0.454 0.0 HOH
 2.719
 O
 O
7bol 1 P62837 93.2 9e-104 X-RAY
 2021-03-24 MET A:39 A:38 69.0 0.373 E -89.2 136.6 69.0 0.373 0.0 HOH
 2.526
 HB3
 O
1w4u 1 P51669 93.2 9e-104 NMR
 2004-11-10 MET A:38 A:38 34.0 0.184 E -123.6 146.5 34.0 0.184 0.0
4a49 2 P62837 93.2 9e-104 X-RAY
 2012-01-25 MET B:38 B:38 85.0 0.459 E -82.2 134.4 85.0 0.459 0.0 HOH
 3.297
 O
 O
4a4b 3 P62837 93.2 9e-104 X-RAY
 2012-01-25 MET C:38 C:38 92.0 0.497 E -80.7 119.3 92.0 0.497 0.0
4a4c 3 P62837 93.2 9e-104 X-RAY
 2012-01-25 MET C:38 C:38 81.0 0.438 E -81.0 143.5 81.0 0.438 0.0
5d1k 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 MET A:38 A:38 82.0 0.443 E -80.1 133.9 82.0 0.443 0.0 HOH
 2.642
 O
 O
5d1l 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 MET A:38 A:38 90.0 0.486 E -74.9 132.1 90.0 0.486 0.0 HOH
 3.565
 CB
 O
5d1m 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 MET A:38 A:38 87.0 0.47 E -77.6 134.5 87.0 0.47 0.0 HOH
 2.795
 O
 O
2clw 1 P62837 93.2 1e-103 X-RAY
 2007-06-12 MET A:56 A:38 77.0 0.416 E -91.8 129.9 77.0 0.416 0.0 HOH
 5.832
 O
 O
2clw 2 P62837 93.2 1e-103 X-RAY
 2007-06-12 MET B:56 B:38 103.0 0.557 E -83.3 133.4 NA NA NA
MET C:56 C:38 62.0 0.335 E -88.5 128.5 NA NA NA
MET D:56 D:38 90.0 0.486 E -87.8 130.3 NA NA NA
3eb6 2 P62840 93.2 1e-103 X-RAY
 2008-09-09 MET B:40 B:38 72.0 0.389 -98.8 84.0 72.0 0.389 0.0
6m2c 1 P62837 93.2 1e-103 X-RAY
 2021-04-07 MET A:40 A:38 76.0 0.411 E -88.2 132.9 76.0 0.411 0.0 HOH
 2.557
 HE2
 O
MET B:40 B:38 51.0 0.276 E -86.1 130.2 NA NA NA
MET C:40 C:38 82.0 0.443 E -87.3 129.3 NA NA NA
MET D:40 D:38 96.0 0.519 E -86.1 131.7 NA NA NA
2esk 1 P62837 93.2 1e-103 X-RAY
 2005-12-06 MET A:40 A:38 79.0 0.427 E -76.9 139.1 79.0 0.427 0.0 HOH
 2.626
 O
 O
3l1y 1 P62837 92.52 2e-103 X-RAY
 2010-05-05 MET A:48 A:38 111.0 0.6 E -79.7 132.4 111.0 0.6 0.0 HOH
 3.413
 CE
 O
3l1z 1 P61077 91.84 4e-103 X-RAY
 2010-05-05 MET A:48 A:38 82.0 0.443 -87.7 14.3 82.0 0.443 0.0
2esq 1 P62837 92.52 5e-103 X-RAY
 2005-12-06 MET A:40 A:38 80.0 0.432 E -71.1 135.8 80.0 0.432 0.0 HOH
 2.777
 O
 O
2eso 1 P62837 92.52 6e-103 X-RAY
 2005-12-06 MET A:40 A:38 80.0 0.432 E -79.0 141.5 80.0 0.432 0.0 HOH
 2.700
 O
 O
2esp 1 P62837 92.52 6e-103 X-RAY
 2005-12-06 MET A:40 A:38 84.0 0.454 E -80.1 138.7 84.0 0.454 0.0 HOH
 2.667
 O
 O
5egg 1 P61077 91.84 8e-103 X-RAY
 2016-11-02 MET A:47 A:38 84.0 0.454 E -86.0 138.4 84.0 0.454 0.0 HOH
 2.959
 N
 O
3a33 1 P62837 92.52 1e-102 X-RAY
 2009-11-24 MET A:41 A:38 51.0 0.276 E -88.6 133.3 51.0 0.276 0.0 HOH
 6.163
 O
 O
1x23 1 P61077 91.84 1e-102 X-RAY
 2005-05-03 MET A:46 A:38 87.0 0.47 E -88.2 136.4 87.0 0.47 0.0 HOH
 2.957
 CE
 O
MET B:46 B:38 72.0 0.389 E -88.5 146.0 NA NA NA
MET C:46 C:38 92.0 0.497 E -82.8 132.8 NA NA NA
MET D:46 D:38 84.0 0.454 E -89.8 139.8 NA NA NA
4ldt 3 P62837 92.52 2e-102 X-RAY
 2013-08-14 MET C:39 C:38 104.0 0.562 E -79.6 129.0 104.0 0.562 0.0 EDO
HOH
 3.629
4.120
 CB
CG
 O1
O
4wz3 1 P62837 92.52 2e-102 X-RAY
 2015-01-07 MET A:39 A:38 71.0 0.384 E -99.1 153.1 71.0 0.384 0.0 HOH
 7.738
 CE
 O
6hpr 3 P62837 92.52 3e-102 X-RAY
 2018-12-12 MET C:38 C:38 54.0 0.292 E -85.5 132.2 2.0 0.011 0.281 B:P0CG47:0.281
 HOH
 3.542
 CG
 O
4ddg 1 P62837,Q96FW1 92.52 4e-102 X-RAY
 2012-02-22 MET A:40 A:38 51.0 0.276 E -88.4 140.1 16.0 0.086 0.19 G:P0CG48:0.189
MET B:40 B:38 50.0 0.27 E -88.4 140.1 15.0 0.081 0.189 H:P0CG48:0.189
MET C:40 C:38 43.0 0.232 E -88.3 140.1 9.0 0.049 0.183 I:P0CG48:0.184
MET J:40 J:38 55.0 0.297 E -88.4 140.1 NA NA NA
MET K:40 K:38 55.0 0.297 E -88.4 140.1 NA NA NA
MET L:40 L:38 47.0 0.254 E -88.4 140.1 NA NA NA
4ddi 1 P62837,Q96FW1 92.52 4e-102 X-RAY
 2012-02-22 MET A:40 A:38 41.0 0.222 E -81.4 139.2 3.0 0.016 0.206 G:P0CG48:0.205
MET B:40 B:38 51.0 0.276 E -81.5 139.3 14.0 0.076 0.2 H:P0CG48:0.2
MET C:40 C:38 49.0 0.265 E -81.5 139.2 13.0 0.07 0.195 I:P0CG48:0.195
5zbu 1 P62837 92.52 4e-102 X-RAY
 2019-02-27 MET A:39 C:38 63.0 0.341 E -85.2 143.4 63.0 0.341 0.0
MET B:39 B:38 97.0 0.524 E -85.3 144.5 NA NA NA
4s3o 1 P61077 91.78 5e-102 X-RAY
 2015-07-15 MET A:39 A:38 105.0 0.568 E -84.9 134.9 NA NA NA
MET B:39 D:38 86.0 0.465 E -77.0 133.7 86.0 0.465 0.0 HOH
 9.346
 C
 O
3rpg 1 P61077 91.78 5e-102 X-RAY
 2011-08-17 MET A:40 A:38 92.0 0.497 E -83.6 137.3 92.0 0.497 0.0 HOH
 3.063
 CB
 O
6cp0 2 P61077 91.16 6e-102 X-RAY
 2018-08-01 MET B:40 B:38 86.0 0.465 E -112.7 125.5 86.0 0.465 0.0
3ugb 1 P61077 91.16 7e-102 X-RAY
 2012-05-16 MET A:38 A:38 62.0 0.335 E -74.1 145.7 62.0 0.335 0.0 HOH
 3.098
 O
 O
4bvu 2 P61077 91.16 7e-102 X-RAY
 2014-01-29 MET B:38 B:38 89.0 0.481 E -89.4 125.3 89.0 0.481 0.0
1z2u 1 P35129 92.52 8e-102 X-RAY
 2005-03-22 MET A:41 A:38 91.0 0.492 E -86.1 135.6 91.0 0.492 0.0 HOH
 2.771
 O
 O
5ifr 1 P61077 91.78 8e-102 X-RAY
 2016-05-11 MET A:42 A:38 69.0 0.373 E -72.0 144.5 69.0 0.373 0.0 HOH
 3.451
 CB
 O
7lyb 7 P61077 91.78 8e-102 EM
 2021-07-28 MET J:56 P:38 86.0 0.465 -117.1 150.6 86.0 0.465 0.0
5mnj 1 P62837 91.84 2e-101 X-RAY
 2017-05-31 MET A:38 A:38 67.0 0.362 E -84.7 140.2 67.0 0.362 0.0 HOH
 8.939
 SD
 O
MET E:38 E:38 89.0 0.481 E -82.5 130.7 NA NA NA
5vzw 1 P62837 91.84 2e-101 X-RAY
 2017-08-09 MET A:38 A:38 73.0 0.395 E -92.8 129.5 73.0 0.395 0.0 HOH
 8.261
 HB2
 O
MET E:38 B:38 55.0 0.297 E -93.1 129.4 55.0 0.297 0.0 HOH
 9.944
 HG3
 O
7ahz 2 Q28EY6 91.84 2e-101 X-RAY
 2021-01-20 MET B:38 BBB:38 96.0 0.519 E -79.7 127.0 NA NA NA
MET E:38 EEE:38 85.0 0.459 E -80.9 129.0 NA NA NA
MET H:38 HHH:38 92.0 0.497 E -78.9 129.0 NA NA NA
MET K:38 KKK:38 108.0 0.584 E -78.0 129.0 NA NA NA
7ai0 2 P62837 91.84 2e-101 X-RAY
 2021-01-20 MET B:38 BBB:38 92.0 0.497 E -84.0 132.9 NA NA NA
MET E:38 EEE:38 76.0 0.411 E -80.7 129.5 NA NA NA
7ai1 2 P62837 91.84 2e-101 X-RAY
 2021-01-20 MET B:38 BBB:38 93.0 0.503 E -80.3 132.4 NA NA NA
MET E:38 EEE:38 94.0 0.508 E -77.5 131.2 NA NA NA
3oj4 1 P51668 91.84 2e-101 X-RAY
 2010-12-08 MET A:44 A:38 92.0 0.497 E -66.9 135.1 7.0 0.038 0.459 B:P0CG47:0.459
MET D:44 D:38 90.0 0.486 E -68.2 134.5 NA NA NA
3ptf 1 P51668 91.84 2e-101 X-RAY
 2011-05-11 MET A:44 A:38 98.0 0.53 E -92.5 137.6 33.0 0.178 0.352 C:P0CG47:0.351
 HOH
 3.509
 CB
 O
MET B:44 B:38 100.0 0.541 E -92.6 136.4 NA NA NA
4r8p 8 Q99496,P61077 91.78 2e-101 X-RAY
 2014-11-05 MET L:159 L:238 36.0 NA E -84.8 -165.7 36.0 NA NA
MET N:159 N:238 33.0 NA -77.9 140.0 33.0 NA NA
4v3l 1 P62837 92.47 2e-101 X-RAY
 2015-04-08 MET A:37 A:38 68.0 0.368 E -85.1 129.3 11.0 0.059 0.309 D:P0CG48:0.308
 HOH
 5.520
 O
 O
2yho 2 P51668 91.84 3e-101 X-RAY
 2011-06-29 MET B:40 B:38 97.0 0.524 E -90.9 120.8 97.0 0.524 0.0 HOH
 3.084
 O
 O
MET D:40 D:38 97.0 0.524 E -89.0 121.1 NA NA NA
MET F:40 F:38 96.0 0.519 E -86.2 123.9 NA NA NA
MET H:40 H:38 95.0 0.514 E -91.7 129.1 NA NA NA
6d4p 1 P51668 91.84 3e-101 X-RAY
 2019-07-17 MET A:40 A:38 99.0 0.535 E -110.8 149.4 9.0 0.049 0.486 B:Q59EM9:0.486
 HOH
 1.967
 H
 O
4qpl 2 P51668 91.84 3e-101 X-RAY
 2014-10-15 MET B:45 B:38 97.0 0.524 E -91.2 126.9 97.0 0.524 0.0 HOH
 4.322
 CG
 O
MET D:45 D:38 82.0 0.443 E -92.2 125.3 NA NA NA
2c4p 1 P51668 91.84 3e-101 X-RAY
 2006-11-22 MET A:56 A:38 83.0 0.449 E -105.2 134.1 83.0 0.449 0.0 HOH
 4.132
 CE
 O
MET B:56 B:38 90.0 0.486 E -102.3 146.3 NA NA NA
4auq 1 P62837 91.16 8e-101 X-RAY
 2012-08-15 MET A:38 A:38 78.0 0.422 E -77.6 136.7 78.0 0.422 0.0 HOH
 6.884
 CG
 O
MET D:38 D:38 71.0 0.384 E -78.2 141.5 71.0 0.384 0.0 HOH
 9.579
 C
 O
3zni 3 P62837 91.78 1e-100 X-RAY
 2013-07-10 MET C:37 C:38 94.0 0.508 E -85.6 130.7 94.0 0.508 0.0 HOH
 5.449
 O
 O
MET G:37 G:38 98.0 0.53 E -88.0 133.1 NA NA NA
MET K:37 K:38 98.0 0.53 E -82.4 125.8 NA NA NA
MET O:37 O:38 78.0 0.422 E -88.7 129.3 NA NA NA
4v3k 1 P62837 91.78 1e-100 X-RAY
 2015-04-08 MET A:37 A:38 60.0 0.324 E -83.3 135.7 NA NA NA
MET D:37 D:38 86.0 0.465 E -78.9 131.7 86.0 0.465 0.0 HOH
 3.825
 CE
 O
6sqo 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 MET B:37 B:38 89.0 0.481 E -80.2 129.6 89.0 0.481 0.0 HOH
 4.547
 CE
 O
MET E:37 E:38 83.0 0.449 E -85.7 130.1 83.0 0.449 0.0 HOH
 3.557
 CB
 O
6sqr 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 MET B:37 B:38 91.0 0.492 E -77.7 131.8 91.0 0.492 0.0 HOH
 3.724
 CG
 O
MET E:37 E:38 89.0 0.481 E -74.5 126.5 89.0 0.481 0.0
MET H:37 H:38 76.0 0.411 E -80.1 127.4 76.0 0.411 0.0 EDO
HOH
 6.785
3.492
 CE
CE
 O1
O
MET K:37 K:38 93.0 0.503 E -79.3 132.2 93.0 0.503 0.0 EDO
HOH
 4.227
3.831
 CE
N
 C1
O
6sqs 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 MET B:37 B:38 90.0 0.486 E -72.5 140.9 90.0 0.486 0.0 HOH
 3.672
 CB
 O
MET E:37 E:38 108.0 0.584 E -71.0 140.2 108.0 0.584 0.0 HOH
 8.727
 CA
 O
5edv 2 P62837 91.78 2e-100 X-RAY
 2016-01-20 MET C:40 C:38 74.0 0.4 E -84.9 134.5 74.0 0.4 0.0
MET D:40 D:38 61.0 0.33 E -85.1 134.4 NA NA NA
MET I:40 I:38 59.0 0.319 E -85.2 134.6 NA NA NA
6ttu 6 P62837 91.16 4e-100 EM
 2020-02-12 MET F:38 D:38 72.0 0.389 E -87.9 126.9 13.0 0.07 0.319 D:Q15843:0.319
3jvz 1 P62837 91.1 6e-100 X-RAY
 2010-01-12 MET A:37 A:38 90.0 0.486 E -87.2 121.8 90.0 0.486 0.0
MET B:37 B:38 100.0 0.541 E -73.0 114.4 NA NA NA
3jw0 1 P62837 91.1 6e-100 X-RAY
 2010-01-12 MET A:37 A:38 96.0 0.519 E -98.6 133.5 96.0 0.519 0.0
MET B:37 B:38 100.0 0.541 E -68.5 115.2 NA NA NA
5tut 1 P51668 91.16 7e-100 X-RAY
 2017-11-08 MET A:41 A:38 96.0 0.519 E -86.4 138.0 96.0 0.519 0.0
7jzv 1 A0A386IN42,P61077 91.1 8e-100 EM
 2021-02-17 MET A:149 A:238 120.0 0.649 E -92.5 141.6 120.0 0.649 0.0
4ap4 2 P51668 90.48 3e-99 X-RAY
 2012-07-25 MET B:44 B:38 92.0 0.497 E -92.1 137.7 92.0 0.497 0.0 HOH
 3.339
 CG
 O
MET D:44 E:38 60.0 0.324 E -93.0 137.6 60.0 0.324 0.0 HOH
 7.215
 O
 O
5fer 2 P51668 90.48 7e-99 X-RAY
 2016-05-18 MET B:41 B:38 85.0 0.459 E -101.1 136.2 85.0 0.459 0.0
MET E:41 E:38 93.0 0.503 E -99.7 142.9 93.0 0.503 0.0
6w7z 1 P62837 90.48 1e-93 X-RAY
 2020-05-20 MET A:43 A:38 86.0 0.465 E -80.2 140.0 86.0 0.465 0.0 HOH
 2.530
 O
 O
5d0k 1 P62837 90.48 3e-93 X-RAY
 2015-12-09 MET A:43 A:38 73.0 0.395 E -76.8 143.7 73.0 0.395 0.0
MET C:43 D:38 50.0 0.27 E -84.5 155.5 NA NA NA
MET E:43 G:38 96.0 0.519 E -74.8 141.6 NA NA NA
MET G:43 J:38 39.0 0.211 E -82.3 139.9 NA NA NA
5ulh 1 P62837 90.48 3e-93 X-RAY
 2017-06-07 MET A:43 A:38 68.0 0.368 E -76.3 137.2 68.0 0.368 0.0 HOH
 2.534
 O
 O
5ulk 1 P62837 90.48 3e-93 X-RAY
 2017-06-07 MET A:43 A:38 63.0 0.341 E -81.1 131.4 8.0 0.043 0.298 B:P0CG47:0.297
6w9d 1 P62837 89.8 1e-92 X-RAY
 2020-05-20 MET A:38 A:38 68.0 0.368 E -83.5 134.9 68.0 0.368 0.0
MET D:38 D:38 54.0 0.292 E -79.6 130.4 NA NA NA
MET G:38 G:38 60.0 0.324 E -84.1 133.8 NA NA NA
5d0m 1 P62837 89.8 2e-92 X-RAY
 2015-12-09 MET A:43 A:38 107.0 0.578 E -81.8 142.2 107.0 0.578 0.0 HOH
 2.686
 O
 O
5ulf 1 P62837 89.8 2e-92 X-RAY
 2017-06-07 MET A:43 A:38 66.0 0.357 E -84.1 138.8 66.0 0.357 0.0 HOH
 3.632
 CE
 O
MET C:43 C:38 79.0 0.427 E -84.2 137.8 NA NA NA
6t7f 2 P61077 89.04 6e-92 X-RAY
 2020-08-05 MET B:41 B:38 64.0 0.346 E -84.9 140.0 64.0 0.346 0.0 HOH
 3.873
 CE
 O
4ii2 3 P46595 82.31 6e-91 X-RAY
 2013-02-13 MET C:38 C:38 90.0 0.486 E -74.8 136.8 90.0 0.486 0.0 HOH
 2.514
 O
 O
5aie 2 P15731 81.25 1e-89 X-RAY
 2015-04-29 MET B:49 B:39 102.0 0.551 E -92.1 145.9 102.0 0.551 0.0
1qcq 1 P15731 81.25 2e-89 X-RAY
 1999-05-17 MET A:39 A:39 85.0 0.459 E -101.0 145.2 85.0 0.459 0.0
2ayv 1 ? 81.38 3e-89 X-RAY
 2005-09-20 MET A:58 A:38 86.0 0.465 E -84.9 132.0 86.0 0.465 0.0 HOH
 9.186
 C
 O
4x57 1 P35131 80.27 3e-89 X-RAY
 2016-01-20 MET A:69 A:38 64.0 0.346 E -92.8 109.5 19.0 0.103 0.243 B:Q9SW27:0.243
 SO4
 7.209
 CE
 O3
MET C:69 C:38 65.0 0.351 E -97.8 110.9 NA NA NA

AlphaFold DB

Entity Residue Monomer View
ID Entity Uniprot Identity Evalue Name Label Auth ASA rASA SS φ ψ
af-q9y2x8-f1 1 Q9Y2X8 100.0 3e-110 MET A:38 A:38 78.0 0.422 E -76.0 134.5
af-p62837-f1 1 P62837 93.2 4e-104 MET A:38 A:38 79.0 0.427 E -75.7 134.6
af-p61077-f1 1 P61077 91.84 2e-103 MET A:38 A:38 79.0 0.427 E -76.0 135.0
af-p51668-f1 1 P51668 91.84 1e-101 MET A:38 A:38 80.0 0.432 E -76.2 134.0