Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr7 43978081 . G A CCDS5474.1:NM_015983.3:c.76Gtc>Atc_NP_057067.1:p.26V>I 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 VAL A:31 A:26 76.0 0.49 S -108.4 75.4 76.0 0.49 0.0
VAL B:31 B:26 71.0 0.458 S -75.5 -82.3 71.0 0.458 0.0
3tgd 1 P62837 93.2 6e-104 X-RAY
2011-08-31 VAL A:31 A:26 92.0 0.594 S -68.6 -48.0 92.0 0.594 0.0 HOH
2.588
O
O
7bol 1 P62837 93.2 9e-104 X-RAY
2021-03-24 VAL A:27 A:26 97.0 0.626 S -98.0 106.4 97.0 0.626 0.0 HOH
2.527
O
O
1w4u 1 P51669 93.2 9e-104 NMR
2004-11-10 VAL A:26 A:26 69.0 0.445 S -98.8 -59.6 69.0 0.445 0.0
4a49 2 P62837 93.2 9e-104 X-RAY
2012-01-25 VAL B:26 B:26 79.0 0.51 E -89.6 118.6 79.0 0.51 0.0 HOH
3.840
CA
O
4a4b 3 P62837 93.2 9e-104 X-RAY
2012-01-25 VAL C:26 C:26 47.0 0.303 E -94.6 134.9 47.0 0.303 0.0 HOH
7.142
CG2
O
4a4c 3 P62837 93.2 9e-104 X-RAY
2012-01-25 VAL C:26 C:26 56.0 0.361 E -108.8 121.0 56.0 0.361 0.0
5d1k 1 P62837 93.2 9e-104 X-RAY
2015-10-28 VAL A:26 A:26 56.0 0.361 E -89.3 114.5 56.0 0.361 0.0 HOH
3.541
CG2
O
5d1l 1 P62837 93.2 9e-104 X-RAY
2015-10-28 VAL A:26 A:26 56.0 0.361 E -85.3 114.7 56.0 0.361 0.0 HOH
3.527
CA
O
5d1m 1 P62837 93.2 9e-104 X-RAY
2015-10-28 VAL A:26 A:26 55.0 0.355 E -85.7 113.6 55.0 0.355 0.0 HOH
2.754
O
O
2clw 1 P62837 93.2 1e-103 X-RAY
2007-06-12 VAL A:44 A:26 58.0 0.374 S -88.3 88.9 58.0 0.374 0.0 HOH
2.823
C
O
2clw 2 P62837 93.2 1e-103 X-RAY
2007-06-12 VAL B:44 B:26 61.0 0.394 S -90.1 99.2 NA NA NA
VAL C:44 C:26 55.0 0.355 S -93.0 89.4 NA NA NA
VAL D:44 D:26 54.0 0.348 S -91.1 104.1 NA NA NA
3eb6 2 P62840 93.2 1e-103 X-RAY
2008-09-09 VAL B:28 B:26 87.0 0.561 S -85.2 -61.4 87.0 0.561 0.0
6m2c 1 P62837 93.2 1e-103 X-RAY
2021-04-07 VAL A:28 A:26 71.0 0.458 S -79.5 93.3 71.0 0.458 0.0 HOH
5.188
C
O
VAL B:28 B:26 106.0 0.684 S -81.0 -67.2 NA NA NA
VAL C:28 C:26 95.0 0.613 S -28.9 -56.6 NA NA NA
VAL D:28 D:26 86.0 0.555 -79.1 117.7 NA NA NA
2esk 1 P62837 93.2 1e-103 X-RAY
2005-12-06 VAL A:28 A:26 90.0 0.581 S -64.4 -35.7 90.0 0.581 0.0 HOH
2.759
O
O
3l1y 1 P62837 92.52 2e-103 X-RAY
2010-05-05 VAL A:36 A:26 98.0 0.632 S -61.9 -53.4 98.0 0.632 0.0 HOH
3.231
N
O
3l1z 1 P61077 91.84 4e-103 X-RAY
2010-05-05 VAL A:36 A:26 72.0 0.465 S -69.8 26.1 72.0 0.465 0.0
2esq 1 P62837 92.52 5e-103 X-RAY
2005-12-06 VAL A:28 A:26 67.0 0.432 E -82.7 103.9 67.0 0.432 0.0 HOH
2.835
O
O
2eso 1 P62837 92.52 6e-103 X-RAY
2005-12-06 VAL A:28 A:26 86.0 0.555 S -70.4 -29.7 86.0 0.555 0.0 HOH
3.102
CG1
O
2esp 1 P62837 92.52 6e-103 X-RAY
2005-12-06 VAL A:28 A:26 87.0 0.561 S -65.8 -38.9 87.0 0.561 0.0 HOH
2.980
O
O
5egg 1 P61077 91.84 8e-103 X-RAY
2016-11-02 VAL A:35 A:26 85.0 0.548 S -125.4 35.0 85.0 0.548 0.0 HOH
2.739
N
O
3a33 1 P62837 92.52 1e-102 X-RAY
2009-11-24 VAL A:29 A:26 91.0 0.587 S -59.5 -48.2 91.0 0.587 0.0 HOH
3.704
O
O
1x23 1 P61077 91.84 1e-102 X-RAY
2005-05-03 VAL A:34 A:26 45.0 0.29 S -109.5 135.7 45.0 0.29 0.0 HOH
2.757
O
O
VAL B:34 B:26 55.0 0.355 E -86.9 114.3 NA NA NA
VAL C:34 C:26 86.0 0.555 S -82.8 -31.8 NA NA NA
VAL D:34 D:26 46.0 0.297 -109.6 133.1 NA NA NA
4ldt 3 P62837 92.52 2e-102 X-RAY
2013-08-14 VAL C:27 C:26 88.0 0.568 S -88.8 -25.5 88.0 0.568 0.0 HOH
2.983
N
O
4wz3 1 P62837 92.52 2e-102 X-RAY
2015-01-07 VAL A:27 A:26 83.0 0.535 S -62.9 -48.3 83.0 0.535 0.0 HOH
3.425
O
O
6hpr 3 P62837 92.52 3e-102 X-RAY
2018-12-12 VAL C:26 C:26 74.0 0.477 E -90.5 116.7 74.0 0.477 0.0 HOH
2.784
O
O
4ddg 1 P62837,Q96FW1 92.52 4e-102 X-RAY
2012-02-22 VAL A:28 A:26 64.0 0.413 E -91.7 110.3 25.0 0.161 0.252 B:P62837+Q96FW1:0.252
VAL B:28 B:26 64.0 0.413 E -91.8 110.3 39.0 0.252 0.161 C:P62837+Q96FW1:0.161
VAL C:28 C:26 64.0 0.413 E -91.8 110.3 21.0 0.135 0.278 A:P62837+Q96FW1:0.277
VAL J:28 J:26 64.0 0.413 E -91.8 110.3 NA NA NA
VAL K:28 K:26 63.0 0.406 E -91.7 110.2 NA NA NA
VAL L:28 L:26 64.0 0.413 E -91.8 110.3 NA NA NA
4ddi 1 P62837,Q96FW1 92.52 4e-102 X-RAY
2012-02-22 VAL A:28 A:26 67.0 0.432 E -101.5 105.1 23.0 0.148 0.284 B:P62837+Q96FW1:0.284
VAL B:28 B:26 66.0 0.426 E -101.5 105.1 29.0 0.187 0.239 C:P62837+Q96FW1:0.239
VAL C:28 C:26 67.0 0.432 E -101.5 105.1 30.0 0.194 0.238 A:P62837+Q96FW1:0.239
5zbu 1 P62837 92.52 4e-102 X-RAY
2019-02-27 VAL A:27 C:26 67.0 0.432 S -62.1 -49.6 67.0 0.432 0.0
VAL B:27 B:26 70.0 0.452 S -70.0 101.0 NA NA NA
4s3o 1 P61077 91.78 5e-102 X-RAY
2015-07-15 VAL A:27 A:26 105.0 0.677 S -75.2 -48.7 NA NA NA
VAL B:27 D:26 59.0 0.381 E -90.2 116.2 59.0 0.381 0.0 HOH
6.169
CG2
O
3rpg 1 P61077 91.78 5e-102 X-RAY
2011-08-17 VAL A:28 A:26 88.0 0.568 S -88.5 2.6 88.0 0.568 0.0 HOH
3.382
CG1
O
6cp0 2 P61077 91.16 6e-102 X-RAY
2018-08-01 VAL B:28 B:26 75.0 0.484 S -121.8 135.9 75.0 0.484 0.0
3ugb 1 P61077 91.16 7e-102 X-RAY
2012-05-16 VAL A:26 A:26 81.0 0.523 S -61.9 -46.8 81.0 0.523 0.0 HOH
3.764
CB
O
4bvu 2 P61077 91.16 7e-102 X-RAY
2014-01-29 VAL B:26 B:26 112.0 0.723 S -93.1 -27.7 112.0 0.723 0.0 HOH
7.282
O
O
1z2u 1 P35129 92.52 8e-102 X-RAY
2005-03-22 VAL A:29 A:26 56.0 0.361 E -94.4 102.6 56.0 0.361 0.0 UNX
UNX
UNX
UNX
UNX
HOH
2.960
8.399
4.270
3.885
6.521
3.847
O
CG2
O
CG1
CG1
C
UNK
UNK
UNK
UNK
UNK
O
5ifr 1 P61077 91.78 8e-102 X-RAY
2016-05-11 VAL A:30 A:26 77.0 0.497 S -62.6 -58.0 77.0 0.497 0.0 HOH
3.591
N
O
7lyb 7 P61077 91.78 8e-102 EM
2021-07-28 VAL J:44 P:26 50.0 0.323 S -100.7 23.3 50.0 0.323 0.0
5mnj 1 P62837 91.84 2e-101 X-RAY
2017-05-31 VAL A:26 A:26 65.0 0.419 S -85.1 120.0 65.0 0.419 0.0 HOH
9.812
CG1
O
VAL E:26 E:26 93.0 0.6 S -71.5 -55.6 NA NA NA
5vzw 1 P62837 91.84 2e-101 X-RAY
2017-08-09 VAL A:26 A:26 72.0 0.465 S -82.9 128.0 72.0 0.465 0.0
VAL E:26 B:26 69.0 0.445 S -82.7 126.7 69.0 0.445 0.0
7ahz 2 Q28EY6 91.84 2e-101 X-RAY
2021-01-20 VAL B:26 BBB:26 60.0 0.387 E -84.7 115.4 NA NA NA
VAL E:26 EEE:26 64.0 0.413 E -82.2 116.8 NA NA NA
VAL H:26 HHH:26 63.0 0.406 E -83.9 115.9 NA NA NA
VAL K:26 KKK:26 60.0 0.387 S -66.4 -51.8 NA NA NA
7ai0 2 P62837 91.84 2e-101 X-RAY
2021-01-20 VAL B:26 BBB:26 85.0 0.548 S -68.3 -52.6 NA NA NA
VAL E:26 EEE:26 61.0 0.394 E -88.9 116.3 NA NA NA
7ai1 2 P62837 91.84 2e-101 X-RAY
2021-01-20 VAL B:26 BBB:26 103.0 0.665 S -51.1 -50.3 NA NA NA
VAL E:26 EEE:26 63.0 0.406 S -64.0 108.2 NA NA NA
3oj4 1 P51668 91.84 2e-101 X-RAY
2010-12-08 VAL A:32 A:26 55.0 0.355 E -92.0 113.3 38.0 0.245 0.11 C:P21580:0.11
VAL D:32 D:26 53.0 0.342 E -92.1 113.6 NA NA NA
3ptf 1 P51668 91.84 2e-101 X-RAY
2011-05-11 VAL A:32 A:26 76.0 0.49 S -66.4 -43.5 71.0 0.458 0.032 C:P0CG47:0.032
HOH
7.610
CG2
O
VAL B:32 B:26 77.0 0.497 S -66.5 -43.1 NA NA NA
4r8p 8 Q99496,P61077 91.78 2e-101 X-RAY
2014-11-05 VAL L:147 L:226 116.0 0.748 S -66.4 -43.0 116.0 0.748 0.0 DT
9.540
CG1
OP2
VAL N:147 N:226 93.0 0.6 S -76.4 -22.1 93.0 0.6 0.0
4v3l 1 P62837 92.47 2e-101 X-RAY
2015-04-08 VAL A:25 A:26 51.0 0.329 E -97.8 124.8 51.0 0.329 0.0 HOH
2.799
O
O
2yho 2 P51668 91.84 3e-101 X-RAY
2011-06-29 VAL B:28 B:26 67.0 0.432 -133.2 139.7 67.0 0.432 0.0 HOH
3.339
O
O
VAL D:28 D:26 63.0 0.406 E -80.6 113.9 NA NA NA
VAL F:28 F:26 64.0 0.413 E -76.8 110.8 NA NA NA
VAL H:28 H:26 75.0 0.484 -132.7 140.6 NA NA NA
6d4p 1 P51668 91.84 3e-101 X-RAY
2019-07-17 VAL A:28 A:26 98.0 0.632 S -66.5 -55.1 71.0 0.458 0.174 B:Q59EM9:0.174
HOH
2.943
HB
O
4qpl 2 P51668 91.84 3e-101 X-RAY
2014-10-15 VAL B:33 B:26 83.0 0.535 E -87.3 103.1 83.0 0.535 0.0 HOH
2.638
O
O
VAL D:33 D:26 50.0 0.323 E -87.7 120.2 NA NA NA
2c4p 1 P51668 91.84 3e-101 X-RAY
2006-11-22 VAL A:44 A:26 66.0 0.426 E -84.6 118.3 66.0 0.426 0.0 HOH
4.583
O
O
VAL B:44 B:26 67.0 0.432 S -85.8 123.1 NA NA NA
4auq 1 P62837 91.16 8e-101 X-RAY
2012-08-15 VAL A:26 A:26 84.0 0.542 S -73.6 -62.3 84.0 0.542 0.0 HOH
3.063
O
O
VAL D:26 D:26 90.0 0.581 S -82.7 -63.2 90.0 0.581 0.0 HOH
3.239
N
O
3zni 3 P62837 91.78 1e-100 X-RAY
2013-07-10 VAL C:25 C:26 61.0 0.394 E -94.0 103.4 61.0 0.394 0.0 HOH
4.490
CG2
O
VAL G:25 G:26 57.0 0.368 E -88.8 113.9 NA NA NA
VAL K:25 K:26 55.0 0.355 E -103.8 110.4 NA NA NA
VAL O:25 O:26 59.0 0.381 E -86.7 111.7 NA NA NA
4v3k 1 P62837 91.78 1e-100 X-RAY
2015-04-08 VAL A:25 A:26 111.0 0.716 -101.1 -4.3 NA NA NA
VAL D:25 D:26 84.0 0.542 S -70.6 -57.1 84.0 0.542 0.0 HOH
3.337
N
O
6sqo 2 P62837 91.78 1e-100 X-RAY
2020-05-06 VAL B:25 B:26 58.0 0.374 E -92.5 111.6 58.0 0.374 0.0 HOH
2.719
O
O
VAL E:25 E:26 58.0 0.374 E -85.4 121.9 58.0 0.374 0.0 HOH
2.964
O
O
6sqr 2 P62837 91.78 1e-100 X-RAY
2020-05-06 VAL B:25 B:26 104.0 0.671 S -95.6 -48.0 56.0 0.361 0.31 K:P62837:0.31
HOH
2.943
O
O
VAL E:25 E:26 56.0 0.361 E -79.2 98.0 56.0 0.361 0.0 HOH
7.502
CG2
O
VAL H:25 H:26 70.0 0.452 S -77.9 93.4 70.0 0.452 0.0
VAL K:25 K:26 83.0 0.535 S -67.9 -59.7 83.0 0.535 0.0 HOH
6.542
N
O
6sqs 2 P62837 91.78 1e-100 X-RAY
2020-05-06 VAL B:25 B:26 82.0 0.529 S -62.8 -50.9 82.0 0.529 0.0 HOH
6.791
CG2
O
VAL E:25 E:26 63.0 0.406 E -77.1 102.6 63.0 0.406 0.0 HOH
8.112
O
O
5edv 2 P62837 91.78 2e-100 X-RAY
2016-01-20 VAL C:28 C:26 88.0 0.568 S -70.0 -49.0 88.0 0.568 0.0
VAL D:28 D:26 89.0 0.574 S -70.0 -49.2 NA NA NA
VAL I:28 I:26 86.0 0.555 S -70.3 -49.8 NA NA NA
6ttu 6 P62837 91.16 4e-100 EM
2020-02-12 VAL F:26 D:26 78.0 0.503 -83.1 -59.0 26.0 0.168 0.335 D:Q15843:0.084
A:Q9Y297:0.252
3jvz 1 P62837 91.1 6e-100 X-RAY
2010-01-12 VAL A:25 A:26 77.0 0.497 -109.2 134.6 77.0 0.497 0.0
VAL B:25 B:26 83.0 0.535 S -77.9 112.5 NA NA NA
3jw0 1 P62837 91.1 6e-100 X-RAY
2010-01-12 VAL A:25 A:26 80.0 0.516 -112.5 146.7 80.0 0.516 0.0
VAL B:25 B:26 79.0 0.51 S -73.9 107.0 NA NA NA
5tut 1 P51668 91.16 7e-100 X-RAY
2017-11-08 VAL A:29 A:26 82.0 0.529 S -69.0 -39.3 82.0 0.529 0.0
7jzv 1 A0A386IN42,P61077 91.1 8e-100 EM
2021-02-17 VAL A:137 A:226 47.0 0.303 -78.6 -45.3 47.0 0.303 0.0
4ap4 2 P51668 90.48 3e-99 X-RAY
2012-07-25 VAL B:32 B:26 60.0 0.387 S -76.7 123.5 60.0 0.387 0.0 HOH
6.179
CG2
O
VAL D:32 E:26 64.0 0.413 S -78.3 122.5 64.0 0.413 0.0 HOH
7.166
CG2
O
5fer 2 P51668 90.48 7e-99 X-RAY
2016-05-18 VAL B:29 B:26 104.0 0.671 S -86.1 -40.2 104.0 0.671 0.0 HOH
2.451
N
O
VAL E:29 E:26 95.0 0.613 S -86.4 -51.0 95.0 0.613 0.0
6w7z 1 P62837 90.48 1e-93 X-RAY
2020-05-20 VAL A:31 A:26 96.0 0.619 S -62.9 -60.6 96.0 0.619 0.0 HOH
3.174
N
O
5d0k 1 P62837 90.48 3e-93 X-RAY
2015-12-09 VAL A:31 A:26 43.0 0.277 E -94.6 110.5 43.0 0.277 0.0
VAL C:31 D:26 44.0 0.284 E -98.8 102.7 NA NA NA
VAL E:31 G:26 40.0 0.258 E -95.8 112.7 NA NA NA
VAL G:31 J:26 42.0 0.271 E -92.2 105.5 NA NA NA
5ulh 1 P62837 90.48 3e-93 X-RAY
2017-06-07 VAL A:31 A:26 43.0 0.277 E -87.9 113.8 43.0 0.277 0.0 HOH
3.697
C
O
5ulk 1 P62837 90.48 3e-93 X-RAY
2017-06-07 VAL A:31 A:26 81.0 0.523 S -62.3 -39.2 57.0 0.368 0.155 B:P0CG47:0.155
6w9d 1 P62837 89.8 1e-92 X-RAY
2020-05-20 VAL A:26 A:26 79.0 0.51 S -85.8 -67.8 79.0 0.51 0.0
VAL D:26 D:26 77.0 0.497 S -74.0 -66.4 NA NA NA
VAL G:26 G:26 77.0 0.497 S -81.2 -61.7 NA NA NA
5d0m 1 P62837 89.8 2e-92 X-RAY
2015-12-09 VAL A:31 A:26 56.0 0.361 E -75.8 89.1 56.0 0.361 0.0 HOH
7.824
CG2
O
5ulf 1 P62837 89.8 2e-92 X-RAY
2017-06-07 VAL A:31 A:26 86.0 0.555 -128.7 29.3 86.0 0.555 0.0 HOH
2.827
O
O
VAL C:31 C:26 87.0 0.561 S -128.1 28.8 NA NA NA
6t7f 2 P61077 89.04 6e-92 X-RAY
2020-08-05 VAL B:29 B:26 84.0 0.542 S -118.4 -13.7 84.0 0.542 0.0 HOH
5.768
C
O
4ii2 3 P46595 82.31 6e-91 X-RAY
2013-02-13 VAL C:26 C:26 55.0 0.355 E -106.4 121.3 55.0 0.355 0.0 HOH
7.306
CG2
O
5aie 2 P15731 81.25 1e-89 X-RAY
2015-04-29 VAL B:37 B:27 71.0 0.458 S -67.4 102.2 71.0 0.458 0.0
1qcq 1 P15731 81.25 2e-89 X-RAY
1999-05-17 VAL A:27 A:27 59.0 0.381 E -99.0 113.0 59.0 0.381 0.0
2ayv 1 ? 81.38 3e-89 X-RAY
2005-09-20 VAL A:46 A:26 56.0 0.361 -120.7 103.4 56.0 0.361 0.0
4x57 1 P35131 80.27 3e-89 X-RAY
2016-01-20 VAL A:57 A:26 69.0 0.445 S -69.0 -50.9 48.0 0.31 0.135 B:Q9SW27:0.135
VAL C:57 C:26 70.0 0.452 S -67.0 -56.6 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 VAL A:26 A:26 62.0 0.4 E -93.2 108.7
af-p62837-f1 1 P62837 93.2 4e-104 VAL A:26 A:26 63.0 0.406 E -93.2 107.4
af-p61077-f1 1 P61077 91.84 2e-103 VAL A:26 A:26 63.0 0.406 E -93.4 108.3
af-p51668-f1 1 P51668 91.84 1e-101 VAL A:26 A:26 62.0 0.4 E -93.4 108.2