Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr10 60121158 . G A CCDS7252.1:NM_003338.4:c.85Gac>Aac_NP_003329.1:p.29D>N 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 ASP A:35 A:29 75.0 0.5 E -84.4 114.8 75.0 0.5 0.0
ASP D:35 D:29 72.0 0.48 E -84.1 114.6 NA NA NA
3ptf 1 P51668 100.0 2e-109 X-RAY
 2011-05-11 ASP A:35 A:29 91.0 0.607 -89.8 110.3 91.0 0.607 0.0 HOH
 8.563
 OD2
 O
ASP B:35 B:29 90.0 0.6 -90.9 109.0 NA NA NA
2yho 2 P51668 100.0 2e-109 X-RAY
 2011-06-29 ASP B:31 B:29 74.0 0.493 -62.9 110.2 74.0 0.493 0.0 HOH
 3.273
 CA
 O
ASP D:31 D:29 75.0 0.5 E -82.5 97.7 NA NA NA
ASP F:31 F:29 77.0 0.513 E -83.1 103.5 NA NA NA
ASP H:31 H:29 69.0 0.46 -83.5 116.2 NA NA NA
6d4p 1 P51668 100.0 2e-109 X-RAY
 2019-07-17 ASP A:31 A:29 77.0 0.513 -106.6 105.7 77.0 0.513 0.0 HOH
 2.096
 H
 O
4qpl 2 P51668 100.0 3e-109 X-RAY
 2014-10-15 ASP B:36 B:29 67.0 0.447 E -98.1 103.2 67.0 0.447 0.0 HOH
 2.709
 OD2
 O
ASP D:36 D:29 46.0 0.307 E -94.2 110.8 NA NA NA
2c4p 1 P51668 100.0 4e-109 X-RAY
 2006-11-22 ASP A:47 A:29 70.0 0.467 E -119.6 102.9 70.0 0.467 0.0 HOH
 2.956
 OD2
 O
ASP B:47 B:29 80.0 0.533 -135.6 99.5 NA NA NA
5tut 1 P51668 99.32 6e-108 X-RAY
 2017-11-08 ASP A:32 A:29 91.0 0.607 -98.2 106.3 91.0 0.607 0.0
4ap4 2 P51668 98.64 2e-107 X-RAY
 2012-07-25 ASP B:35 B:29 84.0 0.56 -103.7 102.9 84.0 0.56 0.0 HOH
 4.099
 N
 O
ASP D:35 E:29 87.0 0.58 -103.0 104.5 87.0 0.58 0.0
5fer 2 P51668 98.64 4e-107 X-RAY
 2016-05-18 ASP B:32 B:29 79.0 0.527 -90.2 106.8 79.0 0.527 0.0 HOH
 3.583
 O
 O
ASP E:32 E:29 75.0 0.5 -86.4 113.1 75.0 0.5 0.0
2oxq 1 Q6PC58 94.56 3e-103 X-RAY
 2008-02-19 ASP A:34 A:29 83.0 0.553 -15.4 111.9 83.0 0.553 0.0
ASP B:34 B:29 82.0 0.547 -89.0 89.1 82.0 0.547 0.0
1z2u 1 P35129 89.12 6e-100 X-RAY
 2005-03-22 ASP A:32 A:29 75.0 0.5 E -94.3 92.9 75.0 0.5 0.0 UNX
UNX
UNX
UNX
HOH
 3.626
4.459
4.020
3.995
4.773
 CB
N
OD2
OD2
N
 UNK
UNK
UNK
UNK
O
3tgd 1 P62837 89.12 1e-99 X-RAY
 2011-08-31 ASP A:34 A:29 84.0 0.56 -88.6 106.7 84.0 0.56 0.0 HOH
 2.448
 OD1
 O
7bol 1 P62837 89.12 1e-99 X-RAY
 2021-03-24 ASP A:30 A:29 79.0 0.527 -84.1 104.8 79.0 0.527 0.0 HOH
 2.338
 H
 O
2esk 1 P62837 89.12 1e-99 X-RAY
 2005-12-06 ASP A:31 A:29 84.0 0.56 -97.0 106.1 84.0 0.56 0.0 HOH
 2.667
 CB
 O
3eb6 2 P62840 89.12 1e-99 X-RAY
 2008-09-09 ASP B:31 B:29 84.0 0.56 -66.5 99.1 84.0 0.56 0.0
6m2c 1 P62837 89.12 1e-99 X-RAY
 2021-04-07 ASP A:31 A:29 73.0 0.487 -83.5 132.5 73.0 0.487 0.0 HOH
 7.293
 H
 O
ASP B:31 B:29 79.0 0.527 -90.9 146.0 NA NA NA
ASP C:31 C:29 73.0 0.487 -90.7 128.6 NA NA NA
ASP D:31 D:29 72.0 0.48 S -91.4 -174.7 NA NA NA
1w4u 1 P51669 89.12 2e-99 NMR
 2004-11-10 ASP A:29 A:29 38.0 0.253 S -86.4 141.1 38.0 0.253 0.0
4a49 2 P62837 89.12 2e-99 X-RAY
 2012-01-25 ASP B:29 B:29 68.0 0.453 E -102.8 108.1 68.0 0.453 0.0 K
HOH
 9.736
3.694
 C
CA
 K
O
4a4b 3 P62837 89.12 2e-99 X-RAY
 2012-01-25 ASP C:29 C:29 82.0 0.547 E -92.1 107.2 82.0 0.547 0.0 HOH
 3.105
 OD2
 O
4a4c 3 P62837 89.12 2e-99 X-RAY
 2012-01-25 ASP C:29 C:29 84.0 0.56 E -91.9 111.2 84.0 0.56 0.0
5d1k 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 ASP A:29 A:29 81.0 0.54 E -91.4 104.3 81.0 0.54 0.0 HOH
 2.582
 OD2
 O
5d1l 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 ASP A:29 A:29 82.0 0.547 E -93.6 103.8 82.0 0.547 0.0 HOH
 2.731
 OD2
 O
5d1m 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 ASP A:29 A:29 80.0 0.533 E -93.6 102.8 80.0 0.533 0.0 HOH
 2.667
 OD2
 O
2clw 1 P62837 89.12 2e-99 X-RAY
 2007-06-12 ASP A:47 A:29 75.0 0.5 -98.0 113.8 75.0 0.5 0.0 HOH
 3.311
 N
 O
2clw 2 P62837 89.12 2e-99 X-RAY
 2007-06-12 ASP B:47 B:29 87.0 0.58 -88.4 120.6 NA NA NA
ASP C:47 C:29 58.0 0.387 -87.9 123.7 NA NA NA
ASP D:47 D:29 78.0 0.52 -93.2 121.2 NA NA NA
3l1y 1 P62837 88.44 3e-99 X-RAY
 2010-05-05 ASP A:39 A:29 71.0 0.473 -108.8 106.7 71.0 0.473 0.0 HOH
 2.838
 O
 O
3l1z 1 P61077 88.44 3e-99 X-RAY
 2010-05-05 ASP A:39 A:29 82.0 0.547 -84.9 121.6 82.0 0.547 0.0
2esq 1 P62837 88.44 7e-99 X-RAY
 2005-12-06 ASP A:31 A:29 80.0 0.533 E -90.7 103.0 80.0 0.533 0.0 HOH
 2.847
 OD1
 O
5egg 1 P61077 88.44 7e-99 X-RAY
 2016-11-02 ASP A:38 A:29 94.0 0.627 -70.4 99.9 94.0 0.627 0.0 HOH
 2.781
 O
 O
2eso 1 P62837 88.44 9e-99 X-RAY
 2005-12-06 ASP A:31 A:29 83.0 0.553 -87.0 102.6 83.0 0.553 0.0 HOH
 2.424
 CB
 O
2esp 1 P62837 88.44 9e-99 X-RAY
 2005-12-06 ASP A:31 A:29 84.0 0.56 -90.5 105.1 84.0 0.56 0.0 HOH
 2.514
 OD1
 O
1x23 1 P61077 88.44 9e-99 X-RAY
 2005-05-03 ASP A:37 A:29 78.0 0.52 -95.0 109.1 78.0 0.52 0.0 HOH
 2.522
 OD2
 O
ASP B:37 B:29 76.0 0.507 E -91.8 99.6 NA NA NA
ASP C:37 C:29 97.0 0.647 -92.3 111.0 NA NA NA
ASP D:37 D:29 84.0 0.56 -98.6 107.8 NA NA NA
3a33 1 P62837 88.44 2e-98 X-RAY
 2009-11-24 ASP A:32 A:29 67.0 0.447 -106.3 104.6 67.0 0.447 0.0 HOH
 2.749
 N
 O
4ldt 3 P62837 88.44 3e-98 X-RAY
 2013-08-14 ASP C:30 C:29 92.0 0.613 -79.2 106.0 92.0 0.613 0.0 HOH
 2.860
 O
 O
4wz3 1 P62837 88.44 3e-98 X-RAY
 2015-01-07 ASP A:30 A:29 87.0 0.58 -62.2 155.6 87.0 0.58 0.0 HOH
 8.009
 N
 O
4s3o 1 P61077 88.36 4e-98 X-RAY
 2015-07-15 ASP A:30 A:29 67.0 0.447 -98.5 108.7 NA NA NA
ASP B:30 D:29 82.0 0.547 E -112.6 104.1 82.0 0.547 0.0
3rpg 1 P61077 88.36 5e-98 X-RAY
 2011-08-17 ASP A:31 A:29 75.0 0.5 -98.9 109.4 75.0 0.5 0.0 HOH
 3.045
 N
 O
6hpr 3 P62837 88.44 5e-98 X-RAY
 2018-12-12 ASP C:29 C:29 53.0 0.353 E -119.8 102.8 53.0 0.353 0.0 HOH
 3.201
 OD2
 O
6cp0 2 P61077 87.76 6e-98 X-RAY
 2018-08-01 ASP B:31 B:29 78.0 0.52 -61.6 130.9 78.0 0.52 0.0
5zbu 1 P62837 88.44 6e-98 X-RAY
 2019-02-27 ASP A:30 C:29 89.0 0.593 -78.9 99.5 89.0 0.593 0.0
ASP B:30 B:29 74.0 0.493 -82.4 101.5 NA NA NA
5ifr 1 P61077 88.36 7e-98 X-RAY
 2016-05-11 ASP A:33 A:29 83.0 0.553 -92.4 111.3 83.0 0.553 0.0 HOH
 2.940
 O
 O
7lyb 7 P61077 88.36 8e-98 EM
 2021-07-28 ASP J:47 P:29 82.0 0.547 -97.0 129.1 82.0 0.547 0.0
4ddg 1 P62837,Q96FW1 88.44 1e-97 X-RAY
 2012-02-22 ASP A:31 A:29 74.0 0.493 E -75.5 122.6 32.0 0.213 0.28 C:P62837+Q96FW1:0.213
B:P62837+Q96FW1:0.067
ASP B:31 B:29 76.0 0.507 E -75.5 122.6 27.0 0.18 0.327 C:P62837+Q96FW1:0.033
A:P62837+Q96FW1:0.293
ASP C:31 C:29 75.0 0.5 E -75.5 122.6 42.0 0.28 0.22 A:P62837+Q96FW1:0.067
B:P62837+Q96FW1:0.147
ASP J:31 J:29 76.0 0.507 E -75.5 122.6 NA NA NA
ASP K:31 K:29 75.0 0.5 E -75.5 122.6 NA NA NA
ASP L:31 L:29 75.0 0.5 E -75.6 122.6 NA NA NA
4ddi 1 P62837,Q96FW1 88.44 1e-97 X-RAY
 2012-02-22 ASP A:31 A:29 74.0 0.493 E -81.2 121.7 20.0 0.133 0.36 C:P62837+Q96FW1:0.273
B:P62837+Q96FW1:0.1
ASP B:31 B:29 75.0 0.5 E -81.2 121.8 19.0 0.127 0.373 C:P62837+Q96FW1:0.087
A:P62837+Q96FW1:0.307
ASP C:31 C:29 74.0 0.493 E -81.1 121.7 14.0 0.093 0.4 A:P62837+Q96FW1:0.1
B:P62837+Q96FW1:0.32
3ugb 1 P61077 87.76 1e-97 X-RAY
 2012-05-16 ASP A:29 A:29 91.0 0.607 -96.5 115.8 91.0 0.607 0.0 GOL
HOH
 9.352
3.176
 OD2
N
 C2
O
4bvu 2 P61077 87.76 1e-97 X-RAY
 2014-01-29 ASP B:29 B:29 86.0 0.573 -119.5 115.7 86.0 0.573 0.0 HOH
 8.293
 N
 O
4r8p 8 Q99496,P61077 88.36 2e-97 X-RAY
 2014-11-05 ASP L:150 L:229 79.0 0.527 -69.3 118.5 79.0 0.527 0.0 DC
DA
DT
DT
 9.521
9.072
6.636
7.272
 OD1
OD1
OD1
OD2
 OP1
O3'
OP1
OP1
ASP N:150 N:229 63.0 0.42 -77.9 133.2 63.0 0.42 0.0 DA
 9.927
 OD2
 OP1
5mnj 1 P62837 87.76 3e-97 X-RAY
 2017-05-31 ASP A:29 A:29 57.0 0.38 -80.6 118.4 57.0 0.38 0.0 HOH
 6.239
 OD2
 O
ASP E:29 E:29 65.0 0.433 -108.3 117.7 NA NA NA
5vzw 1 P62837 87.76 3e-97 X-RAY
 2017-08-09 ASP A:29 A:29 83.0 0.553 -84.8 117.4 83.0 0.553 0.0
ASP E:29 B:29 84.0 0.56 -84.1 117.0 84.0 0.56 0.0
7ahz 2 Q28EY6 87.76 3e-97 X-RAY
 2021-01-20 ASP B:29 BBB:29 87.0 0.58 E -87.1 98.2 NA NA NA
ASP E:29 EEE:29 81.0 0.54 E -86.1 99.6 NA NA NA
ASP H:29 HHH:29 87.0 0.58 E -86.4 98.5 NA NA NA
ASP K:29 KKK:29 83.0 0.553 -90.2 98.7 NA NA NA
7ai0 2 P62837 87.76 3e-97 X-RAY
 2021-01-20 ASP B:29 BBB:29 87.0 0.58 -103.4 103.0 NA NA NA
ASP E:29 EEE:29 77.0 0.513 E -99.1 103.1 NA NA NA
7ai1 2 P62837 87.76 3e-97 X-RAY
 2021-01-20 ASP B:29 BBB:29 92.0 0.613 -86.7 109.4 NA NA NA
ASP E:29 EEE:29 75.0 0.5 -91.1 106.3 NA NA NA
4v3l 1 P62837 88.36 5e-97 X-RAY
 2015-04-08 ASP A:28 A:29 78.0 0.52 E -99.2 106.4 78.0 0.52 0.0 HOH
 3.497
 CB
 O
4auq 1 P62837 87.07 1e-96 X-RAY
 2012-08-15 ASP A:29 A:29 76.0 0.507 -93.2 109.2 76.0 0.507 0.0 HOH
 4.070
 OD2
 O
ASP D:29 D:29 87.0 0.58 -95.3 107.3 87.0 0.58 0.0 HOH
 2.874
 O
 O
3zni 3 P62837 87.67 2e-96 X-RAY
 2013-07-10 ASP C:28 C:29 79.0 0.527 E -84.8 107.0 79.0 0.527 0.0 HOH
 3.876
 CA
 O
ASP G:28 G:29 82.0 0.547 E -80.7 106.9 NA NA NA
ASP K:28 K:29 79.0 0.527 E -90.1 104.3 NA NA NA
ASP O:28 O:29 70.0 0.467 E -93.3 101.3 NA NA NA
4v3k 1 P62837 87.67 2e-96 X-RAY
 2015-04-08 ASP A:28 A:29 71.0 0.473 -118.2 113.8 NA NA NA
ASP D:28 D:29 82.0 0.547 -93.3 109.7 82.0 0.547 0.0 HOH
 2.812
 O
 O
6sqo 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 ASP B:28 B:29 71.0 0.473 E -91.4 99.2 71.0 0.473 0.0 HOH
 2.772
 OD2
 O
ASP E:28 E:29 79.0 0.527 E -94.2 102.0 79.0 0.527 0.0 HOH
 2.727
 OD2
 O
6sqr 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 ASP B:28 B:29 95.0 0.633 -74.6 98.9 42.0 0.28 0.353 J:Q7YRZ8:0.207
K:P62837:0.153
 ZN
HOH
 7.413
2.759
 OD2
OD2
 ZN
O
ASP E:28 E:29 84.0 0.56 E -84.5 108.3 84.0 0.56 0.0
ASP H:28 H:29 90.0 0.6 -74.3 108.7 90.0 0.6 0.0
ASP K:28 K:29 87.0 0.58 -79.6 102.6 87.0 0.58 0.0 HOH
 3.832
 C
 O
6sqs 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 ASP B:28 B:29 87.0 0.58 -96.2 105.4 87.0 0.58 0.0
ASP E:28 E:29 84.0 0.56 E -95.4 103.8 84.0 0.56 0.0 HOH
 3.976
 CA
 O
5edv 2 P62837 87.67 3e-96 X-RAY
 2016-01-20 ASP C:31 C:29 86.0 0.573 -87.2 105.3 86.0 0.573 0.0
ASP D:31 D:29 90.0 0.6 -87.2 105.4 NA NA NA
ASP I:31 I:29 88.0 0.587 -87.2 105.9 NA NA NA
7jzv 1 A0A386IN42,P61077 87.67 5e-96 EM
 2021-02-17 ASP A:140 A:229 94.0 0.627 -164.2 176.6 94.0 0.627 0.0
6ttu 6 P62837 87.07 8e-96 EM
 2020-02-12 ASP F:29 D:29 79.0 0.527 -69.3 99.5 62.0 0.413 0.114 A:Q9Y297:0.113
3jvz 1 P62837 86.99 1e-95 X-RAY
 2010-01-12 ASP A:28 A:29 72.0 0.48 -64.7 131.4 67.0 0.447 0.033 C:Q96PU5:0.033
ASP B:28 B:29 80.0 0.533 -47.9 114.4 NA NA NA
3jw0 1 P62837 86.99 1e-95 X-RAY
 2010-01-12 ASP A:28 A:29 71.0 0.473 -40.6 129.6 68.0 0.453 0.02 C:Q96PU5:0.02
ASP B:28 B:29 77.0 0.513 -69.4 130.2 NA NA NA
6w7z 1 P62837 86.39 2e-89 X-RAY
 2020-05-20 ASP A:34 A:29 85.0 0.567 -91.8 100.9 85.0 0.567 0.0 HOH
 2.864
 O
 O
5d0k 1 P62837 86.39 7e-89 X-RAY
 2015-12-09 ASP A:34 A:29 75.0 0.5 E -96.7 98.8 75.0 0.5 0.0
ASP C:34 D:29 67.0 0.447 E -98.1 97.4 NA NA NA
ASP E:34 G:29 78.0 0.52 E -99.5 97.9 NA NA NA
ASP G:34 J:29 77.0 0.513 E -85.6 103.7 NA NA NA
5ulh 1 P62837 86.39 7e-89 X-RAY
 2017-06-07 ASP A:34 A:29 69.0 0.46 E -104.1 98.1 69.0 0.46 0.0 HOH
 6.565
 OD1
 O
5ulk 1 P62837 86.39 7e-89 X-RAY
 2017-06-07 ASP A:34 A:29 77.0 0.513 -72.9 105.9 77.0 0.513 0.0
6w9d 1 P62837 85.71 2e-88 X-RAY
 2020-05-20 ASP A:29 A:29 86.0 0.573 -102.2 107.9 86.0 0.573 0.0
ASP D:29 D:29 82.0 0.547 -98.7 108.4 NA NA NA
ASP G:29 G:29 86.0 0.573 -96.4 102.7 NA NA NA
5d0m 1 P62837 85.71 3e-88 X-RAY
 2015-12-09 ASP A:34 A:29 82.0 0.547 E -74.1 103.3 82.0 0.547 0.0 HOH
 8.347
 OD2
 O
5ulf 1 P62837 85.71 3e-88 X-RAY
 2017-06-07 ASP A:34 A:29 88.0 0.587 -77.4 99.3 88.0 0.587 0.0 HOH
 2.756
 O
 O
ASP C:34 C:29 88.0 0.587 -77.0 100.2 NA NA NA
6t7f 2 P61077 85.62 5e-88 X-RAY
 2020-08-05 ASP B:32 B:29 80.0 0.533 -76.9 107.6 80.0 0.533 0.0 HOH
 3.582
 N
 O

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 ASP A:29 A:29 85.0 0.567 E -82.0 101.7
af-q9y2x8-f1 1 Q9Y2X8 91.84 1e-101 ASP A:29 A:29 85.0 0.567 E -82.5 102.1
af-p62837-f1 1 P62837 89.12 7e-100 ASP A:29 A:29 84.0 0.56 E -82.5 99.1
af-p61077-f1 1 P61077 88.44 2e-99 ASP A:29 A:29 82.0 0.547 E -82.7 99.5