Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr7 43988274 . A C CCDS5474.1:NM_015983.3:c.242aAt>aCt_NP_057067.1:p.81N>T 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 ASN A:86 A:81 118.0 0.738 T -98.9 6.2 118.0 0.738 0.0 HOH
3.535
OD1
O
ASN B:86 B:81 119.0 0.744 T -104.4 44.4 119.0 0.744 0.0 HOH
3.555
OD1
O
3tgd 1 P62837 93.2 6e-104 X-RAY
2011-08-31 ASN A:86 A:81 125.0 0.781 T -86.8 -2.5 125.0 0.781 0.0 HOH
2.748
O
O
7bol 1 P62837 93.2 9e-104 X-RAY
2021-03-24 ASN A:82 A:81 131.0 0.819 T -90.6 5.5 131.0 0.819 0.0 HOH
2.644
O
O
1w4u 1 P51669 93.2 9e-104 NMR
2004-11-10 ASN A:81 A:81 93.0 0.581 T -120.5 11.1 93.0 0.581 0.0
4a49 2 P62837 93.2 9e-104 X-RAY
2012-01-25 ASN B:81 B:81 127.0 0.794 T -88.6 -0.1 127.0 0.794 0.0 HOH
2.889
O
O
4a4b 3 P62837 93.2 9e-104 X-RAY
2012-01-25 ASN C:81 C:81 122.0 0.762 T -88.5 -10.9 122.0 0.762 0.0
4a4c 3 P62837 93.2 9e-104 X-RAY
2012-01-25 ASN C:81 C:81 128.0 0.8 S -76.6 -18.7 128.0 0.8 0.0
5d1k 1 P62837 93.2 9e-104 X-RAY
2015-10-28 ASN A:81 A:81 130.0 0.812 T -91.4 -0.7 84.0 0.525 0.287 B:Q96BH1:0.287
PEG
HOH
7.012
2.859
N
OD1
C4
O
5d1l 1 P62837 93.2 9e-104 X-RAY
2015-10-28 ASN A:81 A:81 130.0 0.812 T -94.8 1.6 85.0 0.531 0.281 B:Q96BH1:0.281
PEG
HOH
7.372
2.771
N
OD1
O4
O
5d1m 1 P62837 93.2 9e-104 X-RAY
2015-10-28 ASN A:81 A:81 132.0 0.825 T -92.2 -1.5 88.0 0.55 0.275 B:Q96BH1:0.275
PEG
HOH
6.485
2.820
N
O
C4
O
2clw 1 P62837 93.2 1e-103 X-RAY
2007-06-12 ASN A:99 A:81 126.0 0.787 T -85.6 -2.3 126.0 0.787 0.0 GOL
HOH
4.488
3.237
ND2
ND2
O3
O
2clw 2 P62837 93.2 1e-103 X-RAY
2007-06-12 ASN B:99 B:81 135.0 0.844 T -79.0 0.4 NA NA NA
ASN C:99 C:81 126.0 0.787 T -78.9 -7.7 NA NA NA
ASN D:99 D:81 142.0 0.887 T -74.3 -16.1 NA NA NA
3eb6 2 P62840 93.2 1e-103 X-RAY
2008-09-09 ASN B:83 B:81 144.0 0.9 T -99.9 -8.2 144.0 0.9 0.0
6m2c 1 P62837 93.2 1e-103 X-RAY
2021-04-07 ASN A:83 A:81 118.0 0.738 T -94.3 3.8 118.0 0.738 0.0 HOH
3.449
O
O
ASN B:83 B:81 119.0 0.744 T -96.1 4.6 NA NA NA
ASN C:83 C:81 123.0 0.769 T -97.7 6.1 NA NA NA
ASN D:83 D:81 122.0 0.762 T -94.8 3.8 NA NA NA
2esk 1 P62837 93.2 1e-103 X-RAY
2005-12-06 ASN A:83 A:81 129.0 0.806 T -87.1 -3.3 129.0 0.806 0.0 HOH
3.107
O
O
3l1y 1 P62837 92.52 2e-103 X-RAY
2010-05-05 ASN A:91 A:81 130.0 0.812 T -81.8 -1.4 130.0 0.812 0.0 HOH
2.918
OD1
O
3l1z 1 P61077 91.84 4e-103 X-RAY
2010-05-05 ASN A:91 A:81 125.0 0.781 T -69.7 -41.6 125.0 0.781 0.0 HOH
6.693
OD1
O
2esq 1 P62837 92.52 5e-103 X-RAY
2005-12-06 ASN A:83 A:81 128.0 0.8 T -86.6 -2.0 128.0 0.8 0.0 HOH
2.844
ND2
O
2eso 1 P62837 92.52 6e-103 X-RAY
2005-12-06 ASN A:83 A:81 128.0 0.8 T -90.5 -1.9 128.0 0.8 0.0 HOH
2.858
OD1
O
2esp 1 P62837 92.52 6e-103 X-RAY
2005-12-06 ASN A:83 A:81 127.0 0.794 T -86.2 -1.8 127.0 0.794 0.0 HOH
2.934
ND2
O
5egg 1 P61077 91.84 8e-103 X-RAY
2016-11-02 ASN A:90 A:81 135.0 0.844 T -88.3 -7.1 135.0 0.844 0.0 HOH
2.677
OD1
O
3a33 1 P62837 92.52 1e-102 X-RAY
2009-11-24 ASN A:84 A:81 128.0 0.8 T -84.6 3.8 100.0 0.625 0.175 B:P62988:0.175
GOL
HOH
6.589
5.534
O
N
O1
O
1x23 1 P61077 91.84 1e-102 X-RAY
2005-05-03 ASN A:89 A:81 130.0 0.812 T -81.5 -5.5 130.0 0.812 0.0 HOH
2.935
OD1
O
ASN B:89 B:81 146.0 0.912 T -77.6 -8.6 NA NA NA
ASN C:89 C:81 113.0 0.706 T -97.3 9.2 NA NA NA
ASN D:89 D:81 137.0 0.856 T -71.3 -10.4 NA NA NA
4ldt 3 P62837 92.52 2e-102 X-RAY
2013-08-14 ASN C:82 C:81 129.0 0.806 T -88.6 2.5 128.0 0.8 0.006 A:Q96FW1+Q9XVR6:0.006
HOH
3.012
ND2
O
4wz3 1 P62837 92.52 2e-102 X-RAY
2015-01-07 ASN A:82 A:81 129.0 0.806 T -94.3 -6.8 129.0 0.806 0.0 HOH
4.112
C
O
6hpr 3 P62837 92.52 3e-102 X-RAY
2018-12-12 ASN C:81 C:81 135.0 0.844 T -87.9 0.1 135.0 0.844 0.0 HOH
3.011
O
O
4ddg 1 P62837,Q96FW1 92.52 4e-102 X-RAY
2012-02-22 ASN A:83 A:81 133.0 0.831 T -70.2 -27.1 112.0 0.7 0.131 C:P62837+Q96FW1:0.131
ASN B:83 B:81 131.0 0.819 T -70.2 -27.1 114.0 0.713 0.106 A:P62837+Q96FW1:0.106
ASN C:83 C:81 133.0 0.831 T -70.3 -27.0 107.0 0.669 0.162 B:P62837+Q96FW1:0.163
ASN J:83 J:81 133.0 0.831 T -70.3 -27.0 NA NA NA
ASN K:83 K:81 130.0 0.812 T -70.3 -27.1 NA NA NA
ASN L:83 L:81 131.0 0.819 T -70.3 -27.0 NA NA NA
4ddi 1 P62837,Q96FW1 92.52 4e-102 X-RAY
2012-02-22 ASN A:83 A:81 143.0 0.894 T -84.6 -5.5 123.0 0.769 0.125 C:P62837+Q96FW1:0.125
ASN B:83 B:81 145.0 0.906 T -84.5 -5.5 137.0 0.856 0.05 A:P62837+Q96FW1:0.05
ASN C:83 C:81 143.0 0.894 T -84.3 -5.7 137.0 0.856 0.038 B:P62837+Q96FW1:0.037
5zbu 1 P62837 92.52 4e-102 X-RAY
2019-02-27 ASN A:82 C:81 147.0 0.919 S -79.8 -16.2 147.0 0.919 0.0 HOH
3.044
ND2
O
ASN B:82 B:81 120.0 0.75 T -70.2 -23.7 NA NA NA
4s3o 1 P61077 91.78 5e-102 X-RAY
2015-07-15 ASN A:82 A:81 138.0 0.863 T -87.3 -3.7 NA NA NA
ASN B:82 D:81 137.0 0.856 T -84.0 -9.9 137.0 0.856 0.0 HOH
5.541
N
O
3rpg 1 P61077 91.78 5e-102 X-RAY
2011-08-17 ASN A:83 A:81 123.0 0.769 T -88.3 -4.7 123.0 0.769 0.0 HOH
2.743
OD1
O
6cp0 2 P61077 91.16 6e-102 X-RAY
2018-08-01 ASN B:83 B:81 146.0 0.912 T -50.4 -38.7 146.0 0.912 0.0 HOH
2.331
ND2
O
3ugb 1 P61077 91.16 7e-102 X-RAY
2012-05-16 ASN A:81 A:81 134.0 0.838 T -85.6 -0.2 35.0 0.219 0.619 A:P61077:0.619
GOL
HOH
9.485
2.725
OD1
ND2
C3
O
4bvu 2 P61077 91.16 7e-102 X-RAY
2014-01-29 ASN B:81 B:81 140.0 0.875 T -79.6 -0.9 140.0 0.875 0.0 HOH
2.704
ND2
O
1z2u 1 P35129 92.52 8e-102 X-RAY
2005-03-22 ASN A:84 A:81 132.0 0.825 T -87.4 -1.7 132.0 0.825 0.0 HOH
2.696
OD1
O
5ifr 1 P61077 91.78 8e-102 X-RAY
2016-05-11 ASN A:85 A:81 133.0 0.831 T -83.5 -9.7 133.0 0.831 0.0 HOH
2.624
ND2
O
7lyb 7 P61077 91.78 8e-102 EM
2021-07-28 ASN J:99 P:81 129.0 0.806 T -78.0 0.4 129.0 0.806 0.0
5mnj 1 P62837 91.84 2e-101 X-RAY
2017-05-31 ASN A:81 A:81 127.0 0.794 T -86.0 0.1 127.0 0.794 0.0 HOH
3.452
ND2
O
ASN E:81 E:81 122.0 0.762 T -85.2 -5.4 NA NA NA
5vzw 1 P62837 91.84 2e-101 X-RAY
2017-08-09 ASN A:81 A:81 129.0 0.806 T -80.6 0.3 129.0 0.806 0.0 HOH
2.315
HD22
O
ASN E:81 B:81 131.0 0.819 T -79.9 1.3 131.0 0.819 0.0
7ahz 2 Q28EY6 91.84 2e-101 X-RAY
2021-01-20 ASN B:81 BBB:81 131.0 0.819 T -84.9 -3.4 NA NA NA
ASN E:81 EEE:81 117.0 0.731 T -91.3 5.6 NA NA NA
ASN H:81 HHH:81 127.0 0.794 T -86.2 -3.1 NA NA NA
ASN K:81 KKK:81 130.0 0.812 T -84.0 -5.0 NA NA NA
7ai0 2 P62837 91.84 2e-101 X-RAY
2021-01-20 ASN B:81 BBB:81 149.0 0.931 T -95.6 5.8 NA NA NA
ASN E:81 EEE:81 140.0 0.875 T -103.1 11.8 NA NA NA
7ai1 2 P62837 91.84 2e-101 X-RAY
2021-01-20 ASN B:81 BBB:81 130.0 0.812 T -76.7 -6.3 NA NA NA
ASN E:81 EEE:81 137.0 0.856 T -79.9 -3.6 NA NA NA
3oj4 1 P51668 91.84 2e-101 X-RAY
2010-12-08 ASN A:87 A:81 134.0 0.838 T -78.6 5.1 134.0 0.838 0.0
ASN D:87 D:81 135.0 0.844 T -78.4 4.9 NA NA NA
3ptf 1 P51668 91.84 2e-101 X-RAY
2011-05-11 ASN A:87 A:81 131.0 0.819 T -95.1 1.9 131.0 0.819 0.0 HOH
4.459
C
O
ASN B:87 B:81 135.0 0.844 T -91.0 9.2 NA NA NA
4r8p 8 Q99496,P61077 91.78 2e-101 X-RAY
2014-11-05 ASN L:202 L:281 131.0 0.819 S -72.9 -40.7 131.0 0.819 0.0 DC
DG
DA
DG
DT
DC
DT
DC
DG
DA
6.599
5.541
8.396
9.269
9.903
5.219
4.097
3.610
5.408
6.575
O
OD1
OD1
ND2
ND2
ND2
ND2
OD1
OD1
N
N4
O6
N1
N2
O3'
C2'
OP2
N4
O6
N6
ASN N:202 N:281 137.0 0.856 S -97.8 -33.8 137.0 0.856 0.0 DC
DC
DG
DA
DT
DC
DG
9.145
7.015
7.401
9.710
3.768
4.378
7.985
ND2
ND2
ND2
ND2
OD1
ND2
ND2
C5
N4
O6
N6
C7
N4
O6
4v3l 1 P62837 92.47 2e-101 X-RAY
2015-04-08 ASN A:80 A:81 130.0 0.812 T -92.8 -0.9 130.0 0.812 0.0 EDO
HOH
5.647
3.045
N
O
O2
O
2yho 2 P51668 91.84 3e-101 X-RAY
2011-06-29 ASN B:83 B:81 130.0 0.812 T -86.7 -5.0 130.0 0.812 0.0 ACT
ACT
HOH
7.396
3.712
2.543
O
C
ND2
CH3
O
O
ASN D:83 D:81 125.0 0.781 T -91.2 -5.2 NA NA NA
ASN F:83 F:81 125.0 0.781 T -85.8 2.1 NA NA NA
ASN H:83 H:81 127.0 0.794 T -87.0 -0.6 NA NA NA
6d4p 1 P51668 91.84 3e-101 X-RAY
2019-07-17 ASN A:83 A:81 128.0 0.8 T -84.3 2.8 128.0 0.8 0.0 HOH
6.416
H
O
4qpl 2 P51668 91.84 3e-101 X-RAY
2014-10-15 ASN B:88 B:81 133.0 0.831 T -83.3 -6.5 133.0 0.831 0.0 HOH
3.004
O
O
ASN D:88 D:81 132.0 0.825 T -84.7 -4.0 NA NA NA
2c4p 1 P51668 91.84 3e-101 X-RAY
2006-11-22 ASN A:99 A:81 99.0 0.619 T -107.8 11.2 99.0 0.619 0.0 HOH
3.931
OD1
O
ASN B:99 B:81 119.0 0.744 T -86.7 -3.7 NA NA NA
4auq 1 P62837 91.16 8e-101 X-RAY
2012-08-15 ASN A:81 A:81 133.0 0.831 T -91.5 1.4 133.0 0.831 0.0 HOH
3.508
C
O
ASN D:81 D:81 132.0 0.825 T -85.6 1.8 132.0 0.825 0.0 HOH
2.590
OD1
O
3zni 3 P62837 91.78 1e-100 X-RAY
2013-07-10 ASN C:80 C:81 136.0 0.85 T -82.2 -9.6 136.0 0.85 0.0 HOH
2.741
O
O
ASN G:80 G:81 141.0 0.881 T -83.8 -8.6 NA NA NA
ASN K:80 K:81 141.0 0.881 T -90.1 -3.5 NA NA NA
ASN O:80 O:81 132.0 0.825 T -83.3 -8.1 NA NA NA
4v3k 1 P62837 91.78 1e-100 X-RAY
2015-04-08 ASN A:80 A:81 125.0 0.781 T -88.2 -1.3 NA NA NA
ASN D:80 D:81 129.0 0.806 T -89.5 -1.0 129.0 0.806 0.0 CL
HOH
3.241
3.078
ND2
O
CL
O
6sqo 2 P62837 91.78 1e-100 X-RAY
2020-05-06 ASN B:80 B:81 135.0 0.844 T -104.3 16.2 135.0 0.844 0.0 HOH
2.827
OD1
O
ASN E:80 E:81 147.0 0.919 T -89.4 5.8 147.0 0.919 0.0 HOH
3.204
N
O
6sqr 2 P62837 91.78 1e-100 X-RAY
2020-05-06 ASN B:80 B:81 131.0 0.819 T -91.8 4.8 131.0 0.819 0.0 HOH
3.331
O
O
ASN E:80 E:81 128.0 0.8 T -91.6 2.8 128.0 0.8 0.0 HOH
9.405
C
O
ASN H:80 H:81 124.0 0.775 T -82.6 -1.0 124.0 0.775 0.0 HOH
3.205
O
O
ASN K:80 K:81 125.0 0.781 T -89.4 0.9 125.0 0.781 0.0 EDO
HOH
3.620
2.906
C
O
C1
O
6sqs 2 P62837 91.78 1e-100 X-RAY
2020-05-06 ASN B:80 B:81 140.0 0.875 T -82.5 -7.3 140.0 0.875 0.0 HOH
3.069
OD1
O
ASN E:80 E:81 143.0 0.894 T -81.6 -9.2 143.0 0.894 0.0 HOH
4.989
N
O
5edv 2 P62837 91.78 2e-100 X-RAY
2016-01-20 ASN C:83 C:81 131.0 0.819 T -86.8 -1.6 131.0 0.819 0.0
ASN D:83 D:81 131.0 0.819 T -86.8 -1.6 NA NA NA
ASN I:83 I:81 132.0 0.825 T -86.9 -1.5 NA NA NA
6ttu 6 P62837 91.16 4e-100 EM
2020-02-12 ASN F:81 D:81 132.0 0.825 T -70.0 3.6 87.0 0.544 0.281 A:Q9Y297:0.281
3jvz 1 P62837 91.1 6e-100 X-RAY
2010-01-12 ASN A:80 A:81 125.0 0.781 T -93.0 -13.1 124.0 0.775 0.006 C:Q96PU5:0.006
ASN B:80 B:81 126.0 0.787 T -75.5 24.6 NA NA NA
3jw0 1 P62837 91.1 6e-100 X-RAY
2010-01-12 ASN A:80 A:81 120.0 0.75 S -75.6 -22.2 116.0 0.725 0.025 C:Q96PU5:0.025
ASN B:80 B:81 128.0 0.8 T -87.0 1.7 NA NA NA
5tut 1 P51668 91.16 7e-100 X-RAY
2017-11-08 ASN A:84 A:81 115.0 0.719 T -101.5 10.8 115.0 0.719 0.0
7jzv 1 A0A386IN42,P61077 91.1 8e-100 EM
2021-02-17 ASN A:192 A:281 107.0 0.669 T -91.4 6.5 107.0 0.669 0.0
4ap4 2 P51668 90.48 3e-99 X-RAY
2012-07-25 ASN B:87 B:81 133.0 0.831 T -84.2 2.8 133.0 0.831 0.0 HOH
2.624
ND2
O
ASN D:87 E:81 137.0 0.856 T -86.1 5.9 137.0 0.856 0.0 HOH
5.252
N
O
5fer 2 P51668 90.48 7e-99 X-RAY
2016-05-18 ASN B:84 B:81 135.0 0.844 T -83.2 7.7 135.0 0.844 0.0 HOH
9.769
O
O
ASN E:84 E:81 130.0 0.812 T -81.9 1.2 130.0 0.812 0.0 HOH
6.742
O
O
6w7z 1 P62837 90.48 1e-93 X-RAY
2020-05-20 ASN A:86 A:81 131.0 0.819 T -90.4 2.2 131.0 0.819 0.0 GOL
HOH
7.016
2.771
O
OD1
O2
O
5d0k 1 P62837 90.48 3e-93 X-RAY
2015-12-09 ASN A:86 A:81 129.0 0.806 T -92.4 -2.1 129.0 0.806 0.0
ASN C:86 D:81 126.0 0.787 T -87.5 -0.4 NA NA NA
ASN E:86 G:81 132.0 0.825 T -87.5 -3.7 NA NA NA
ASN G:86 J:81 125.0 0.781 T -88.9 0.3 NA NA NA
5ulh 1 P62837 90.48 3e-93 X-RAY
2017-06-07 ASN A:86 A:81 124.0 0.775 T -89.6 -3.6 124.0 0.775 0.0 GOL
SCN
HOH
6.559
3.614
5.041
O
C
N
O3
N
O
5ulk 1 P62837 90.48 3e-93 X-RAY
2017-06-07 ASN A:86 A:81 141.0 0.881 T 95.6 -31.0 141.0 0.881 0.0
6w9d 1 P62837 89.8 1e-92 X-RAY
2020-05-20 ASN A:81 A:81 123.0 0.769 T -84.3 3.7 123.0 0.769 0.0
ASN D:81 D:81 118.0 0.738 T -83.3 3.3 NA NA NA
ASN G:81 G:81 120.0 0.75 T -81.2 0.6 NA NA NA
5d0m 1 P62837 89.8 2e-92 X-RAY
2015-12-09 ASN A:86 A:81 130.0 0.812 T -98.4 10.6 130.0 0.812 0.0 HOH
2.654
O
O
5ulf 1 P62837 89.8 2e-92 X-RAY
2017-06-07 ASN A:86 A:81 133.0 0.831 T -89.5 3.5 133.0 0.831 0.0 GOL
GOL
HOH
7.092
2.555
2.650
O
OD1
O
O2
O1
O
ASN C:86 C:81 133.0 0.831 T -89.6 3.7 NA NA NA
6t7f 2 P61077 89.04 6e-92 X-RAY
2020-08-05 ASN B:84 B:81 124.0 0.775 T -102.5 -0.7 124.0 0.775 0.0 HOH
5.287
N
O
4ii2 3 P46595 82.31 6e-91 X-RAY
2013-02-13 ASN C:81 C:81 116.0 0.725 T -91.0 -15.2 62.0 0.388 0.337 A:O94609:0.338
HOH
3.262
ND2
O
5aie 2 P15731 81.25 1e-89 X-RAY
2015-04-29 ASN B:92 B:82 124.0 0.775 T -88.1 -12.6 124.0 0.775 0.0
1qcq 1 P15731 81.25 2e-89 X-RAY
1999-05-17 ASN A:82 A:82 126.0 0.787 T -90.6 -2.9 126.0 0.787 0.0
2ayv 1 ? 81.38 3e-89 X-RAY
2005-09-20 GLN A:101 A:81 155.0 0.861 T -92.8 4.2 155.0 0.861 0.0 UNX
UNX
HOH
5.530
8.024
5.107
N
OE1
N
UNK
UNK
O
4x57 1 P35131 80.27 3e-89 X-RAY
2016-01-20 ASN A:112 A:81 123.0 0.769 T -101.5 18.2 123.0 0.769 0.0
ASN C:112 C:81 121.0 0.756 T -105.0 18.3 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 ASN A:81 A:81 127.0 0.794 T -89.9 4.6
af-p62837-f1 1 P62837 93.2 4e-104 ASN A:81 A:81 129.0 0.806 T -90.2 3.5
af-p61077-f1 1 P61077 91.84 2e-103 ASN A:81 A:81 129.0 0.806 T -89.1 4.8
af-p51668-f1 1 P51668 91.84 1e-101 ASN A:81 A:81 128.0 0.8 T -88.0 0.8