Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr10 60121116 . C A CCDS7252.1:NM_003338.4:c.43Cgc>Agc_NP_003329.1:p.15R>S Homo sapiens ubiquitin conjugating enzyme E2 D1 (UBE2D1), transcript variant 1, 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)
3oj4 1 P51668 100.0 2e-109 X-RAY
 2010-12-08 ARG A:21 A:15 163.0 0.724 H -86.4 -47.7 163.0 0.724 0.0
ARG D:21 D:15 164.0 0.729 H -85.7 -48.4 NA NA NA
3ptf 1 P51668 100.0 2e-109 X-RAY
 2011-05-11 ARG A:21 A:15 198.0 0.88 H -70.7 -32.4 198.0 0.88 0.0 HOH
 8.485
 N
 O
ARG B:21 B:15 199.0 0.884 H -70.4 -33.7 NA NA NA
2yho 2 P51668 100.0 2e-109 X-RAY
 2011-06-29 ARG B:17 B:15 155.0 0.689 H -76.5 -32.4 96.0 0.427 0.262 A:Q8WY64:0.262
 HOH
 3.427
 NH2
 O
ARG D:17 D:15 204.0 0.907 H -73.4 -40.6 NA NA NA
ARG F:17 F:15 198.0 0.88 H -73.3 -37.4 NA NA NA
ARG H:17 H:15 163.0 0.724 H -69.8 -43.4 NA NA NA
6d4p 1 P51668 100.0 2e-109 X-RAY
 2019-07-17 ARG A:17 A:15 208.0 0.924 H -71.5 -31.0 208.0 0.924 0.0 HOH
 2.828
 HD3
 O
4qpl 2 P51668 100.0 3e-109 X-RAY
 2014-10-15 ARG B:22 B:15 149.0 0.662 H -69.6 -45.0 149.0 0.662 0.0 HOH
 3.817
 CD
 O
ARG D:22 D:15 147.0 0.653 H -71.8 -38.8 NA NA NA
2c4p 1 P51668 100.0 4e-109 X-RAY
 2006-11-22 ARG A:33 A:15 181.0 0.804 T -61.4 -37.8 181.0 0.804 0.0 HOH
 3.378
 NE
 O
ARG B:33 B:15 192.0 0.853 T 174.6 -36.4 NA NA NA
5tut 1 P51668 99.32 6e-108 X-RAY
 2017-11-08 ARG A:18 A:15 153.0 0.68 H -74.8 -34.4 153.0 0.68 0.0
4ap4 2 P51668 98.64 2e-107 X-RAY
 2012-07-25 ARG B:21 B:15 171.0 0.76 H -76.4 -49.3 171.0 0.76 0.0 HOH
 5.301
 O
 O
ARG D:21 E:15 168.0 0.747 H -76.6 -48.4 165.0 0.733 0.014 E:F5H7Y5:0.013
 HOH
 5.241
 O
 O
5fer 2 P51668 98.64 4e-107 X-RAY
 2016-05-18 ARG B:18 B:15 185.0 0.822 H -95.2 -10.1 170.0 0.756 0.066 A:Q14258:0.067
ARG E:18 E:15 220.0 0.978 H -65.5 -32.9 220.0 0.978 0.0
2oxq 1 Q6PC58 94.56 3e-103 X-RAY
 2008-02-19 ARG A:20 A:15 198.0 0.88 T -80.4 -46.0 192.0 0.853 0.027 C:Q7ZTZ6:0.027
ARG B:20 B:15 180.0 0.8 H -86.4 -21.4 147.0 0.653 0.147 D:Q7ZTZ6:0.147
1z2u 1 P35129 89.12 6e-100 X-RAY
 2005-03-22 ARG A:18 A:15 201.0 0.893 H -80.4 -28.8 201.0 0.893 0.0 CL
BU3
HOH
 3.127
2.956
3.326
 NH1
NH2
NE
 CL
O5
O
3tgd 1 P62837 89.12 1e-99 X-RAY
 2011-08-31 ARG A:20 A:15 186.0 0.827 H -68.5 -35.1 186.0 0.827 0.0 HOH
 2.795
 NH2
 O
7bol 1 P62837 89.12 1e-99 X-RAY
 2021-03-24 ARG A:16 A:15 194.0 0.862 H -86.1 -19.3 194.0 0.862 0.0 HOH
 2.678
 HB3
 O
2esk 1 P62837 89.12 1e-99 X-RAY
 2005-12-06 ARG A:17 A:15 151.0 0.671 H -74.0 -33.9 151.0 0.671 0.0 HOH
 2.632
 O
 O
3eb6 2 P62840 89.12 1e-99 X-RAY
 2008-09-09 ARG B:17 B:15 207.0 0.92 H -59.2 -47.9 138.0 0.613 0.307 A:Q13489:0.307
6m2c 1 P62837 89.12 1e-99 X-RAY
 2021-04-07 ARG A:17 A:15 226.0 1.0 H -117.6 -29.2 226.0 1.0 0.0 HOH
 4.594
 HG3
 O
ARG B:17 B:15 194.0 0.862 H -112.1 -26.7 NA NA NA
ARG C:17 C:15 165.0 0.733 T -113.2 -36.5 NA NA NA
ARG D:17 D:15 169.0 0.751 H -112.3 -32.3 NA NA NA
1w4u 1 P51669 89.12 2e-99 NMR
 2004-11-10 ARG A:15 A:15 200.0 0.889 H -60.8 -48.0 200.0 0.889 0.0
4a49 2 P62837 89.12 2e-99 X-RAY
 2012-01-25 ARG B:15 B:15 206.0 0.916 H -67.1 -46.1 141.0 0.627 0.289 A:P22681:0.289
 HOH
 4.573
 CG
 O
4a4b 3 P62837 89.12 2e-99 X-RAY
 2012-01-25 ARG C:15 C:15 175.0 0.778 H -75.0 -60.8 128.0 0.569 0.209 A:P22681:0.209
4a4c 3 P62837 89.12 2e-99 X-RAY
 2012-01-25 ARG C:15 C:15 180.0 0.8 H -48.1 -69.7 120.0 0.533 0.267 A:P22681:0.267
5d1k 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 ARG A:15 A:15 169.0 0.751 H -101.1 -17.6 156.0 0.693 0.058 B:Q96BH1:0.058
 HOH
 4.670
 NH2
 O
5d1l 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 ARG A:15 A:15 180.0 0.8 H -70.3 -43.1 160.0 0.711 0.089 B:Q96BH1:0.089
 HOH
 2.699
 NH1
 O
5d1m 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 ARG A:15 A:15 172.0 0.764 H -103.2 -15.5 158.0 0.702 0.062 B:Q96BH1:0.062
 HOH
 2.742
 NH1
 O
2clw 1 P62837 89.12 2e-99 X-RAY
 2007-06-12 ARG A:33 A:15 188.0 0.836 S -79.2 -2.8 188.0 0.836 0.0 HOH
 2.438
 O
 O
2clw 2 P62837 89.12 2e-99 X-RAY
 2007-06-12 ARG B:33 B:15 218.0 0.969 H -77.9 -7.1 NA NA NA
ARG C:33 C:15 206.0 0.916 H -79.9 -13.1 NA NA NA
ARG D:33 D:15 202.0 0.898 H -76.8 -10.1 NA NA NA
3l1y 1 P62837 88.44 3e-99 X-RAY
 2010-05-05 ARG A:25 A:15 178.0 0.791 H -79.2 -27.3 178.0 0.791 0.0 HOH
 5.342
 O
 O
3l1z 1 P61077 88.44 3e-99 X-RAY
 2010-05-05 ARG A:25 A:15 216.0 0.96 S -69.2 -4.9 216.0 0.96 0.0 HOH
 8.153
 NH1
 O
2esq 1 P62837 88.44 7e-99 X-RAY
 2005-12-06 ARG A:17 A:15 222.0 0.987 H -78.6 -24.2 222.0 0.987 0.0 HOH
 4.549
 CB
 O
5egg 1 P61077 88.44 7e-99 X-RAY
 2016-11-02 ARG A:24 A:15 198.0 0.88 H -82.0 -22.8 198.0 0.88 0.0 HOH
 6.289
 C
 O
2eso 1 P62837 88.44 9e-99 X-RAY
 2005-12-06 ARG A:17 A:15 217.0 0.964 H -81.2 -22.3 217.0 0.964 0.0 HOH
 3.410
 NH2
 O
2esp 1 P62837 88.44 9e-99 X-RAY
 2005-12-06 ARG A:17 A:15 153.0 0.68 H -75.2 -31.6 153.0 0.68 0.0 HOH
 2.625
 O
 O
1x23 1 P61077 88.44 9e-99 X-RAY
 2005-05-03 ARG A:23 A:15 163.0 0.724 H -75.8 -37.7 163.0 0.724 0.0 HOH
 2.204
 NH1
 O
ARG B:23 B:15 174.0 0.773 H -70.3 -26.6 NA NA NA
ARG C:23 C:15 165.0 0.733 H -76.1 -38.9 NA NA NA
ARG D:23 D:15 205.0 0.911 H -70.1 -33.3 NA NA NA
3a33 1 P62837 88.44 2e-98 X-RAY
 2009-11-24 ARG A:18 A:15 164.0 0.729 H -67.6 -49.9 164.0 0.729 0.0 HOH
 7.507
 N
 O
4ldt 3 P62837 88.44 3e-98 X-RAY
 2013-08-14 ARG C:16 C:15 176.0 0.782 H -82.3 -26.7 176.0 0.782 0.0 HOH
 2.742
 O
 O
4wz3 1 P62837 88.44 3e-98 X-RAY
 2015-01-07 ARG A:16 A:15 160.0 0.711 T -109.1 -51.2 122.0 0.542 0.169 B:Q5X159:0.169
 HOH
 3.694
 NH2
 O
4s3o 1 P61077 88.36 4e-98 X-RAY
 2015-07-15 ARG A:16 A:15 219.0 0.973 H -84.5 -32.3 NA NA NA
ARG B:16 D:15 209.0 0.929 H -85.8 -40.3 179.0 0.796 0.133 D:Q99496:0.133
 HOH
 5.927
 NH1
 O
3rpg 1 P61077 88.36 5e-98 X-RAY
 2011-08-17 ARG A:17 A:15 184.0 0.818 H -88.6 -25.0 137.0 0.609 0.209 B:P35226:0.013
C:Q99496:0.2
 HOH
 6.574
 NE
 O
6hpr 3 P62837 88.44 5e-98 X-RAY
 2018-12-12 ARG C:15 C:15 180.0 0.8 H -63.7 -38.7 114.0 0.507 0.293 B:P0CG47:0.04
A:Q13490:0.249
 HOH
 3.233
 O
 O
6cp0 2 P61077 87.76 6e-98 X-RAY
 2018-08-01 ARG B:17 B:15 197.0 0.876 H -64.4 -48.9 197.0 0.876 0.0
5zbu 1 P62837 88.44 6e-98 X-RAY
 2019-02-27 ARG A:16 C:15 199.0 0.884 H -72.1 -36.9 199.0 0.884 0.0 HOH
 6.492
 C
 O
ARG B:16 B:15 211.0 0.938 H -71.5 -34.4 NA NA NA
5ifr 1 P61077 88.36 7e-98 X-RAY
 2016-05-11 ARG A:19 A:15 180.0 0.8 H -68.6 -43.9 180.0 0.8 0.0 HOH
 5.259
 CD
 O
7lyb 7 P61077 88.36 8e-98 EM
 2021-07-28 ARG J:33 P:15 211.0 0.938 S -76.3 -0.0 150.0 0.667 0.271 I:P38398:0.271
4ddg 1 P62837,Q96FW1 88.44 1e-97 X-RAY
 2012-02-22 ARG A:17 A:15 182.0 0.809 H -61.1 -54.2 182.0 0.809 0.0
ARG B:17 B:15 181.0 0.804 H -61.1 -54.2 181.0 0.804 0.0
ARG C:17 C:15 182.0 0.809 H -61.0 -54.3 182.0 0.809 0.0
ARG J:17 J:15 182.0 0.809 H -61.1 -54.2 NA NA NA
ARG K:17 K:15 183.0 0.813 H -61.0 -54.3 NA NA NA
ARG L:17 L:15 181.0 0.804 H -61.1 -54.3 NA NA NA
4ddi 1 P62837,Q96FW1 88.44 1e-97 X-RAY
 2012-02-22 ARG A:17 A:15 156.0 0.693 H -56.3 -41.1 156.0 0.693 0.0
ARG B:17 B:15 171.0 0.76 H -56.4 -41.0 171.0 0.76 0.0
ARG C:17 C:15 169.0 0.751 H -56.3 -41.1 169.0 0.751 0.0
3ugb 1 P61077 87.76 1e-97 X-RAY
 2012-05-16 ARG A:15 A:15 180.0 0.8 H -68.7 -46.4 180.0 0.8 0.0 HOH
 6.852
 NH1
 O
4bvu 2 P61077 87.76 1e-97 X-RAY
 2014-01-29 ARG B:15 B:15 182.0 0.809 H -80.6 -62.1 182.0 0.809 0.0
4r8p 8 Q99496,P61077 88.36 2e-97 X-RAY
 2014-11-05 ARG L:136 L:215 77.0 NA H -63.2 -52.7 77.0 NA NA
ARG N:136 N:215 141.0 0.627 H -79.3 -39.6 141.0 0.627 0.0
5mnj 1 P62837 87.76 3e-97 X-RAY
 2017-05-31 ARG A:15 A:15 77.0 NA H -74.3 -69.1 77.0 NA NA
ARG E:15 E:15 84.0 NA H -76.2 -46.4 NA NA NA
5vzw 1 P62837 87.76 3e-97 X-RAY
 2017-08-09 ARG A:15 A:15 166.0 0.738 H -73.7 -49.6 166.0 0.738 0.0
ARG E:15 B:15 166.0 0.738 H -73.0 -49.1 166.0 0.738 0.0 HOH
 2.885
 HG3
 O
7ahz 2 Q28EY6 87.76 3e-97 X-RAY
 2021-01-20 ARG B:15 BBB:15 163.0 0.724 H -71.3 -38.5 NA NA NA
ARG E:15 EEE:15 222.0 0.987 H -69.7 -38.7 NA NA NA
ARG H:15 HHH:15 163.0 0.724 H -71.3 -38.5 NA NA NA
ARG K:15 KKK:15 180.0 0.8 H -71.2 -38.8 NA NA NA
7ai0 2 P62837 87.76 3e-97 X-RAY
 2021-01-20 ARG B:15 BBB:15 161.0 0.716 H -76.8 -31.8 NA NA NA
ARG E:15 EEE:15 210.0 0.933 H -76.7 -32.3 NA NA NA
7ai1 2 P62837 87.76 3e-97 X-RAY
 2021-01-20 ARG B:15 BBB:15 186.0 0.827 H -85.7 -39.0 NA NA NA
ARG E:15 EEE:15 163.0 0.724 H -87.6 -28.4 NA NA NA
4v3l 1 P62837 88.36 5e-97 X-RAY
 2015-04-08 ARG A:14 A:15 90.0 NA H -79.9 -33.0 90.0 NA NA HOH
 4.002
 O
 O
4auq 1 P62837 87.07 1e-96 X-RAY
 2012-08-15 ARG A:15 A:15 200.0 0.889 H -77.6 -47.1 164.0 0.729 0.16 B:Q96CA5:0.16
 HOH
 4.083
 O
 O
ARG D:15 D:15 84.0 NA H -76.6 -28.4 84.0 NA NA HOH
 8.623
 O
 O
3zni 3 P62837 87.67 2e-96 X-RAY
 2013-07-10 ARG C:14 C:15 187.0 0.831 H -64.6 -45.5 130.0 0.578 0.253 A:Q13191:0.253
 HOH
 8.240
 N
 O
ARG G:14 G:15 168.0 0.747 H -75.5 -36.9 NA NA NA
ARG K:14 K:15 193.0 0.858 H -69.5 -45.0 NA NA NA
ARG O:14 O:15 168.0 0.747 H -70.7 -46.7 NA NA NA
4v3k 1 P62837 87.67 2e-96 X-RAY
 2015-04-08 ARG A:14 A:15 198.0 0.88 H -74.3 -52.4 NA NA NA
ARG D:14 D:15 180.0 0.8 H -69.9 -36.9 180.0 0.8 0.0 HOH
 2.981
 NH2
 O
6sqo 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 ARG B:14 B:15 195.0 0.867 H -113.1 -14.5 195.0 0.867 0.0 HOH
 6.618
 N
 O
ARG E:14 E:15 165.0 0.733 H -84.9 -45.7 165.0 0.733 0.0 HOH
 5.888
 NH1
 O
6sqr 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 ARG B:14 B:15 179.0 0.796 H -90.8 -26.2 179.0 0.796 0.0 HOH
 2.750
 O
 O
ARG E:14 E:15 180.0 0.8 H -81.7 -31.8 178.0 0.791 0.009 F:J3QTR3:0.009
 HOH
 6.187
 C
 O
ARG H:14 H:15 220.0 0.978 H -65.7 -18.8 220.0 0.978 0.0 HOH
 9.887
 NH2
 O
ARG K:14 K:15 177.0 0.787 H -94.2 -36.8 177.0 0.787 0.0 HOH
 3.428
 NH1
 O
6sqs 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 ARG B:14 B:15 174.0 0.773 H -73.4 -43.8 174.0 0.773 0.0 HOH
 3.966
 CG
 O
ARG E:14 E:15 178.0 0.791 H -71.8 -43.4 178.0 0.791 0.0 HOH
 9.426
 NH1
 O
5edv 2 P62837 87.67 3e-96 X-RAY
 2016-01-20 ARG C:17 C:15 203.0 0.902 H -69.1 -34.4 203.0 0.902 0.0
ARG D:17 D:15 205.0 0.911 H -68.6 -34.9 NA NA NA
ARG I:17 I:15 209.0 0.929 H -68.8 -34.6 NA NA NA
7jzv 1 A0A386IN42,P61077 87.67 5e-96 EM
 2021-02-17 ARG A:126 A:215 175.0 0.778 H -81.5 -30.6 175.0 0.778 0.0
6ttu 6 P62837 87.07 8e-96 EM
 2020-02-12 ARG F:15 D:15 155.0 0.689 H -99.5 -57.8 102.0 0.453 0.236 C:Q13616:0.236
3jvz 1 P62837 86.99 1e-95 X-RAY
 2010-01-12 ARG A:14 A:15 165.0 0.733 G -132.9 -37.5 165.0 0.733 0.0
ARG B:14 B:15 193.0 0.858 H -66.3 -8.7 NA NA NA
3jw0 1 P62837 86.99 1e-95 X-RAY
 2010-01-12 ARG A:14 A:15 216.0 0.96 H -92.2 -43.1 216.0 0.96 0.0
ARG B:14 B:15 187.0 0.831 H -126.3 -22.1 NA NA NA
6w7z 1 P62837 86.39 2e-89 X-RAY
 2020-05-20 ARG A:20 A:15 230.0 1.0 H -81.8 -37.4 230.0 1.0 0.0 HOH
 5.464
 NH1
 O
5d0k 1 P62837 86.39 7e-89 X-RAY
 2015-12-09 ARG A:20 A:15 201.0 0.893 H -60.4 -30.9 201.0 0.893 0.0
ARG C:20 D:15 177.0 0.787 H -71.5 -27.2 NA NA NA
ARG E:20 G:15 173.0 0.769 H -67.1 -19.5 NA NA NA
ARG G:20 J:15 169.0 0.751 H -66.6 -21.3 NA NA NA
5ulh 1 P62837 86.39 7e-89 X-RAY
 2017-06-07 ARG A:20 A:15 168.0 0.747 H -71.4 -40.8 168.0 0.747 0.0 GOL
HOH
 5.730
6.138
 N
C
 O1
O
5ulk 1 P62837 86.39 7e-89 X-RAY
 2017-06-07 ARG A:20 A:15 183.0 0.813 H -55.9 -48.4 181.0 0.804 0.009 C:Q6ZSG1:0.009
6w9d 1 P62837 85.71 2e-88 X-RAY
 2020-05-20 ARG A:15 A:15 147.0 0.653 H -78.0 -41.4 147.0 0.653 0.0
ARG D:15 D:15 154.0 0.684 H -73.4 -38.1 NA NA NA
ARG G:15 G:15 159.0 0.707 H -76.0 -44.7 NA NA NA
5d0m 1 P62837 85.71 3e-88 X-RAY
 2015-12-09 ARG A:20 A:15 85.0 NA H -74.9 -34.6 85.0 NA NA HOH
 6.726
 N
 O
5ulf 1 P62837 85.71 3e-88 X-RAY
 2017-06-07 ARG A:20 A:15 175.0 0.778 H -76.1 -28.5 175.0 0.778 0.0 HOH
 4.183
 CG
 O
ARG C:20 C:15 159.0 0.707 H -76.4 -28.0 NA NA NA
6t7f 2 P61077 85.62 5e-88 X-RAY
 2020-08-05 ARG B:18 B:15 173.0 0.769 T -113.3 48.1 173.0 0.769 0.0

AlphaFold DB

Entity Residue Monomer View
ID Entity Uniprot Identity Evalue Name Label Auth ASA rASA SS φ ψ
af-p51668-f1 1 P51668 100.0 8e-110 ARG A:15 A:15 188.0 0.836 H -77.8 -40.3
af-q9y2x8-f1 1 Q9Y2X8 91.84 1e-101 ARG A:15 A:15 204.0 0.907 H -77.4 -39.6
af-p62837-f1 1 P62837 89.12 7e-100 ARG A:15 A:15 217.0 0.964 H -80.4 -39.7
af-p61077-f1 1 P61077 88.44 2e-99 ARG A:15 A:15 195.0 0.867 H -81.1 -41.5