Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr4 103720097 . C A CCDS3661.1:NM_181892.3:c.436Gct>Tct_NP_871621.1:p.146A>S Homo sapiens ubiquitin conjugating enzyme E2 D3 (UBE2D3), transcript variant 8, 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)
3l1z 1 P61077 97.96 3e-108 X-RAY
 2010-05-05 ALA A:156 A:146 5.0 0.043 -106.2 23.7 5.0 0.043 0.0 HOH
 7.043
 N
 O
5egg 1 P61077 97.96 6e-108 X-RAY
 2016-11-02 ALA A:155 A:146 8.0 0.07 -122.1 8.3 8.0 0.07 0.0 HOH
 3.157
 O
 O
1x23 1 P61077 97.96 7e-108 X-RAY
 2005-05-03 ALA A:154 A:146 1.0 0.009 -114.5 11.7 1.0 0.009 0.0 HOH
 3.741
 O
 O
ALA B:154 B:146 6.0 0.052 -109.9 11.9 NA NA NA
ALA C:154 C:146 6.0 0.052 -113.4 9.8 NA NA NA
ALA D:154 D:146 6.0 0.052 -114.0 13.0 NA NA NA
3rpg 1 P61077 97.95 3e-107 X-RAY
 2011-08-17 ALA A:148 A:146 7.0 0.061 -113.0 10.8 7.0 0.061 0.0 HOH
 3.668
 O
 O
4s3o 1 P61077 97.95 3e-107 X-RAY
 2015-07-15 ALA A:147 A:146 8.0 0.07 -113.5 3.0 NA NA NA
ALA B:147 D:146 4.0 0.035 -100.3 43.2 4.0 0.035 0.0 HOH
 4.157
 CB
 O
6cp0 2 P61077 97.28 4e-107 X-RAY
 2018-08-01 ALA B:148 B:146 4.0 0.035 T -127.7 30.9 4.0 0.035 0.0
5ifr 1 P61077 97.95 4e-107 X-RAY
 2016-05-11 ALA A:150 A:146 4.0 0.035 -108.9 11.0 4.0 0.035 0.0 HOH
 3.421
 O
 O
3ugb 1 P61077 97.28 6e-107 X-RAY
 2012-05-16 ALA A:146 A:146 6.0 0.052 I -107.4 -19.0 6.0 0.052 0.0 HOH
 2.731
 O
 O
4bvu 2 P61077 97.28 6e-107 X-RAY
 2014-01-29 ALA B:146 B:146 4.0 0.035 -112.2 22.8 4.0 0.035 0.0 HOH
 4.061
 CB
 O
7lyb 7 P61077 97.95 7e-107 EM
 2021-07-28 ALA J:164 P:146 26.0 0.226 H -135.7 -14.3 26.0 0.226 0.0
4r8p 8 Q99496,P61077 97.95 7e-107 X-RAY
 2014-11-05 ALA L:267 L:346 23.0 0.2 T -130.1 -55.2 23.0 0.2 0.0
ALA N:267 N:346 28.0 0.243 T -125.7 -58.1 28.0 0.243 0.0
3tgd 1 P62837 96.6 8e-107 X-RAY
 2011-08-31 ALA A:151 A:146 8.0 0.07 -126.3 11.2 8.0 0.07 0.0 HOH
 3.011
 O
 O
7bol 1 P62837 96.6 8e-107 X-RAY
 2021-03-24 ALA A:147 A:146 6.0 0.052 -124.7 18.1 6.0 0.052 0.0 HOH
 2.882
 HA
 O
1w4u 1 P51669 96.6 9e-107 NMR
 2004-11-10 ALA A:146 A:146 17.0 0.148 I -99.4 -97.7 17.0 0.148 0.0
4a49 2 P62837 96.6 9e-107 X-RAY
 2012-01-25 ALA B:146 B:146 7.0 0.061 -102.2 0.6 7.0 0.061 0.0 HOH
 3.920
 O
 O
4a4b 3 P62837 96.6 9e-107 X-RAY
 2012-01-25 ALA C:146 C:146 9.0 0.078 I -98.9 -4.2 9.0 0.078 0.0
4a4c 3 P62837 96.6 9e-107 X-RAY
 2012-01-25 ALA C:146 C:146 10.0 0.087 I -57.8 -49.6 10.0 0.087 0.0
5d1k 1 P62837 96.6 9e-107 X-RAY
 2015-10-28 ALA A:146 A:146 12.0 0.104 I -111.3 2.1 4.0 0.035 0.069 B:Q96BH1:0.07
 PEG
EDO
HOH
 9.909
9.873
2.785
 N
N
O
 O1
O1
O
5d1l 1 P62837 96.6 9e-107 X-RAY
 2015-10-28 ALA A:146 A:146 13.0 0.113 T -111.8 3.6 5.0 0.043 0.07 B:Q96BH1:0.07
 OXL
HOH
 9.500
3.006
 N
O
 O4
O
5d1m 1 P62837 96.6 9e-107 X-RAY
 2015-10-28 ALA A:146 A:146 13.0 0.113 -114.2 4.7 4.0 0.035 0.078 B:Q96BH1:0.078
 EDO
HOH
 9.790
2.919
 N
O
 O2
O
2esk 1 P62837 96.6 9e-107 X-RAY
 2005-12-06 ALA A:148 A:146 4.0 0.035 -115.3 15.1 4.0 0.035 0.0 HOH
 3.203
 O
 O
3eb6 2 P62840 96.6 1e-106 X-RAY
 2008-09-09 ALA B:148 B:146 10.0 0.087 I -77.1 -53.8 10.0 0.087 0.0
6m2c 1 P62837 96.6 1e-106 X-RAY
 2021-04-07 ALA A:148 A:146 10.0 0.087 I -78.4 -61.3 10.0 0.087 0.0 HOH
 8.099
 HB1
 O
ALA B:148 B:146 15.0 0.13 -78.3 135.2 NA NA NA
ALA C:148 C:146 11.0 0.096 I -78.4 -49.5 NA NA NA
ALA D:148 D:146 13.0 0.113 I -81.0 -42.4 NA NA NA
2clw 1 P62837 96.6 1e-106 X-RAY
 2007-06-12 ALA A:164 A:146 5.0 0.043 -103.9 10.5 5.0 0.043 0.0 HOH
 4.169
 CB
 O
2clw 2 P62837 96.6 1e-106 X-RAY
 2007-06-12 ALA B:164 B:146 2.0 0.017 -107.7 4.9 NA NA NA
ALA C:164 C:146 1.0 0.009 -98.5 3.8 NA NA NA
ALA D:164 D:146 6.0 0.052 -105.4 -6.2 NA NA NA
3l1y 1 P62837 95.92 2e-106 X-RAY
 2010-05-05 ALA A:156 A:146 5.0 0.043 -121.4 18.1 5.0 0.043 0.0 HOH
 3.317
 N
 O
2eso 1 P62837 95.92 4e-106 X-RAY
 2005-12-06 ALA A:148 A:146 4.0 0.035 -111.0 11.4 4.0 0.035 0.0 HOH
 3.449
 C
 O
2esp 1 P62837 95.92 4e-106 X-RAY
 2005-12-06 ALA A:148 A:146 4.0 0.035 -116.6 12.2 4.0 0.035 0.0 HOH
 3.207
 O
 O
2esq 1 P62837 95.92 4e-106 X-RAY
 2005-12-06 ALA A:148 A:146 4.0 0.035 -110.4 12.3 4.0 0.035 0.0 HOH
 3.434
 C
 O
3a33 1 P62837 95.92 1e-105 X-RAY
 2009-11-24 ALA A:149 A:146 5.0 0.043 -113.6 7.3 5.0 0.043 0.0 HOH
 3.189
 O
 O
4ldt 3 P62837 95.92 1e-105 X-RAY
 2013-08-14 ALA C:147 C:146 5.0 0.043 -117.2 11.3 5.0 0.043 0.0 EDO
HOH
 6.392
4.254
 O
CB
 O1
O
4wz3 1 P62837 95.92 1e-105 X-RAY
 2015-01-07 ALA A:147 A:146 15.0 0.13 -88.1 133.2 15.0 0.13 0.0 HOH
 2.625
 O
 O
4ddg 1 P62837,Q96FW1 95.92 1e-105 X-RAY
 2012-02-22 ALA A:148 A:146 3.0 0.026 I -89.0 -12.4 3.0 0.026 0.0
ALA B:148 B:146 1.0 0.009 I -89.0 -12.4 1.0 0.009 0.0
ALA C:148 C:146 1.0 0.009 I -88.8 -12.4 1.0 0.009 0.0
ALA J:148 J:146 3.0 0.026 I -89.0 -12.4 NA NA NA
ALA K:148 K:146 1.0 0.009 I -88.8 -12.5 NA NA NA
ALA L:148 L:146 1.0 0.009 I -89.0 -12.4 NA NA NA
4ddi 1 P62837,Q96FW1 95.92 1e-105 X-RAY
 2012-02-22 ALA A:148 A:146 1.0 0.009 I -82.2 -44.8 1.0 0.009 0.0
ALA B:148 B:146 4.0 0.035 I -82.3 -44.7 4.0 0.035 0.0
ALA C:148 C:146 3.0 0.026 I -82.3 -44.7 3.0 0.026 0.0
5zbu 1 P62837 95.92 2e-105 X-RAY
 2019-02-27 ALA A:147 C:146 7.0 0.061 I -71.2 -36.3 7.0 0.061 0.0
ALA B:147 B:146 69.0 0.6 -81.1 360.0 NA NA NA
7jzv 1 A0A386IN42,P61077 97.26 2e-105 EM
 2021-02-17 ALA A:257 A:346 11.0 0.096 -53.5 -39.5 11.0 0.096 0.0
6hpr 3 P62837 95.92 3e-105 X-RAY
 2018-12-12 ALA C:146 C:146 7.0 0.061 -116.5 14.3 2.0 0.017 0.044 B:P0CG47:0.043
 HOH
 3.313
 O
 O
5mnj 1 P62837 95.24 2e-104 X-RAY
 2017-05-31 ALA A:146 A:146 1.0 0.009 -99.8 4.8 1.0 0.009 0.0 HOH
 3.785
 O
 O
ALA E:146 E:146 7.0 0.061 -86.5 2.5 NA NA NA
5vzw 1 P62837 95.24 2e-104 X-RAY
 2017-08-09 ALA A:146 A:146 9.0 0.078 H -118.3 20.0 9.0 0.078 0.0 HOH
 5.629
 HB2
 O
ALA E:146 B:146 10.0 0.087 H -119.5 20.1 10.0 0.087 0.0
7ahz 2 Q28EY6 95.24 2e-104 X-RAY
 2021-01-20 ALA B:146 BBB:146 7.0 0.061 H -109.5 4.7 NA NA NA
ALA E:146 EEE:146 6.0 0.052 H -109.2 5.2 NA NA NA
ALA H:146 HHH:146 8.0 0.07 H -108.9 7.0 NA NA NA
ALA K:146 KKK:146 7.0 0.061 -108.7 4.7 NA NA NA
7ai0 2 P62837 95.24 2e-104 X-RAY
 2021-01-20 ALA B:146 BBB:146 5.0 0.043 -113.9 19.7 NA NA NA
ALA E:146 EEE:146 8.0 0.07 -122.6 17.5 NA NA NA
7ai1 2 P62837 95.24 2e-104 X-RAY
 2021-01-20 ALA B:146 BBB:146 4.0 0.035 -120.3 17.8 NA NA NA
ALA E:146 EEE:146 5.0 0.043 H -117.9 14.6 NA NA NA
4v3l 1 P62837 95.89 2e-104 X-RAY
 2015-04-08 ALA A:145 A:146 8.0 0.07 -101.2 2.5 4.0 0.035 0.035 D:P0CG48:0.035
 HOH
 3.404
 O
 O
4auq 1 P62837 94.56 7e-104 X-RAY
 2012-08-15 ALA A:146 A:146 2.0 0.017 -97.8 3.3 2.0 0.017 0.0 HOH
 4.469
 CB
 O
ALA D:146 D:146 8.0 0.07 -100.2 3.6 8.0 0.07 0.0 HOH
 4.185
 CB
 O
3zni 3 P62837 95.21 1e-103 X-RAY
 2013-07-10 ALA C:145 C:146 6.0 0.052 -115.5 10.2 6.0 0.052 0.0 HOH
 3.386
 O
 O
ALA G:145 G:146 4.0 0.035 -123.8 12.8 NA NA NA
ALA K:145 K:146 2.0 0.017 -111.8 24.7 NA NA NA
ALA O:145 O:146 5.0 0.043 -119.7 19.2 NA NA NA
4v3k 1 P62837 95.21 1e-103 X-RAY
 2015-04-08 ALA A:145 A:146 7.0 0.061 -100.4 3.8 NA NA NA
ALA D:145 D:146 7.0 0.061 -100.1 3.8 7.0 0.061 0.0 HOH
 3.433
 O
 O
6sqo 2 P62837 95.21 1e-103 X-RAY
 2020-05-06 ALA B:145 B:146 7.0 0.061 -116.9 20.3 7.0 0.061 0.0 HOH
 3.361
 N
 O
ALA E:145 E:146 5.0 0.043 -114.0 25.9 5.0 0.043 0.0 HOH
 2.741
 O
 O
6sqr 2 P62837 95.21 1e-103 X-RAY
 2020-05-06 ALA B:145 B:146 2.0 0.017 -111.4 24.4 2.0 0.017 0.0 HOH
 3.842
 CA
 O
ALA E:145 E:146 2.0 0.017 -118.0 33.2 2.0 0.017 0.0 HOH
 6.394
 N
 O
ALA H:145 H:146 8.0 0.07 -120.6 15.5 8.0 0.07 0.0 HOH
 4.220
 CB
 O
ALA K:145 K:146 4.0 0.035 -118.5 11.9 4.0 0.035 0.0 EDO
EDO
HOH
 9.899
8.739
3.695
 CB
O
CA
 O1
C2
O
6sqs 2 P62837 95.21 1e-103 X-RAY
 2020-05-06 ALA B:145 B:146 4.0 0.035 -118.6 18.6 4.0 0.035 0.0 HOH
 3.708
 CA
 O
ALA E:145 E:146 10.0 0.087 H -118.8 11.7 10.0 0.087 0.0 HOH
 3.739
 O
 O
5edv 2 P62837 95.21 2e-103 X-RAY
 2016-01-20 ALA C:148 C:146 7.0 0.061 I -92.4 -17.3 7.0 0.061 0.0
ALA D:148 D:146 14.0 0.122 I -88.1 -11.1 NA NA NA
ALA I:148 I:146 41.0 0.357 -122.9 360.0 NA NA NA
6ttu 6 P62837 94.56 3e-103 EM
 2020-02-12 ALA F:146 D:146 16.0 0.139 I -56.7 -57.0 4.0 0.035 0.104 D:Q15843:0.104
1z2u 1 P35129 93.2 4e-103 X-RAY
 2005-03-22 ALA A:149 A:146 5.0 0.043 -114.8 7.7 5.0 0.043 0.0 CL
BU3
HOH
 8.355
8.153
3.360
 N
N
C
 CL
C1
O
3jvz 1 P62837 94.52 5e-103 X-RAY
 2010-01-12 ALA A:145 A:146 9.0 0.078 I -92.0 -31.3 9.0 0.078 0.0
ALA B:145 B:146 11.0 0.096 I -85.6 -19.3 NA NA NA
3jw0 1 P62837 94.52 5e-103 X-RAY
 2010-01-12 ALA A:145 A:146 6.0 0.052 -93.3 2.4 6.0 0.052 0.0
ALA B:145 B:146 8.0 0.07 -66.9 -22.0 NA NA NA
2oxq 1 Q6PC58 91.16 4e-102 X-RAY
 2008-02-19 ALA A:151 A:146 8.0 0.07 H -125.9 22.9 8.0 0.07 0.0
ALA B:151 B:146 9.0 0.078 -122.7 5.7 9.0 0.078 0.0
3oj4 1 P51668 88.44 3e-99 X-RAY
 2010-12-08 ALA A:152 A:146 11.0 0.096 T -109.5 -21.4 2.0 0.017 0.079 B:P0CG47:0.078
ALA D:152 D:146 10.0 0.087 T -110.9 -20.0 NA NA NA
3ptf 1 P51668 88.44 3e-99 X-RAY
 2011-05-11 ALA A:152 A:146 5.0 0.043 -119.1 10.5 1.0 0.009 0.034 C:P0CG47:0.035
 HOH
 3.360
 CA
 O
ALA B:152 B:146 5.0 0.043 -106.6 -0.5 NA NA NA
2yho 2 P51668 88.44 3e-99 X-RAY
 2011-06-29 ALA B:148 B:146 5.0 0.043 -122.8 20.4 5.0 0.043 0.0 ACT
HOH
 9.977
3.499
 N
C
 CH3
O
ALA D:148 D:146 6.0 0.052 -127.3 17.0 NA NA NA
ALA F:148 F:146 7.0 0.061 -129.9 20.9 NA NA NA
ALA H:148 H:146 4.0 0.035 -116.3 24.0 NA NA NA
6d4p 1 P51668 88.44 3e-99 X-RAY
 2019-07-17 ALA A:148 A:146 8.0 0.07 -121.5 7.3 2.0 0.017 0.053 B:Q59EM9:0.052
 HOH
 2.795
 HA
 O
4qpl 2 P51668 88.44 5e-99 X-RAY
 2014-10-15 ALA B:153 B:146 7.0 0.061 H -122.7 12.7 7.0 0.061 0.0 HOH
 3.612
 CA
 O
ALA D:153 D:146 8.0 0.07 H -123.3 7.7 NA NA NA
2c4p 1 P51668 88.44 5e-99 X-RAY
 2006-11-22 ALA A:164 A:146 3.0 0.026 -127.6 13.1 3.0 0.026 0.0 HOH
 5.469
 CB
 O
ALA B:164 B:146 2.0 0.017 -131.2 13.9 NA NA NA
5tut 1 P51668 87.76 1e-97 X-RAY
 2017-11-08 ALA A:149 A:146 5.0 0.043 I -103.9 -2.2 5.0 0.043 0.0
6t7f 2 P61077 95.21 3e-97 X-RAY
 2020-08-05 ALA B:149 B:146 8.0 0.07 -122.2 12.9 8.0 0.07 0.0 HOH
 4.905
 CB
 O
4ap4 2 P51668 87.07 5e-97 X-RAY
 2012-07-25 ALA B:152 B:146 6.0 0.052 -119.3 13.8 6.0 0.052 0.0 HOH
 3.385
 O
 O
ALA D:152 E:146 7.0 0.061 -119.0 7.7 7.0 0.061 0.0 HOH
 4.000
 CB
 O
5fer 2 P51668 87.07 1e-96 X-RAY
 2016-05-18 ALA B:149 NA:NA DO NA DO DO DO NA NA NA
ALA E:149 E:146 76.0 0.661 -160.4 360.0 76.0 0.661 0.0 HOH
 7.018
 N
 O
6w7z 1 P62837 93.88 1e-96 X-RAY
 2020-05-20 ALA A:151 A:146 8.0 0.07 -112.5 9.4 8.0 0.07 0.0 HOH
 3.549
 O
 O
5d0k 1 P62837 93.88 2e-96 X-RAY
 2015-12-09 ALA A:151 A:146 2.0 0.017 -110.8 5.2 2.0 0.017 0.0
ALA C:151 D:146 5.0 0.043 H -115.4 5.9 NA NA NA
ALA E:151 G:146 4.0 0.035 -112.8 4.2 NA NA NA
ALA G:151 J:146 5.0 0.043 -108.9 2.0 NA NA NA
5ulh 1 P62837 93.88 2e-96 X-RAY
 2017-06-07 ALA A:151 A:146 6.0 0.052 T -119.2 9.7 6.0 0.052 0.0 SCN
HOH
 9.693
3.273
 CB
O
 S
O
5ulk 1 P62837 93.88 2e-96 X-RAY
 2017-06-07 ALA A:151 A:146 6.0 0.052 T -106.7 3.4 1.0 0.009 0.043 B:P0CG47:0.043
6w9d 1 P62837 93.24 2e-96 X-RAY
 2020-05-20 ALA A:146 A:146 16.0 0.139 S -141.2 10.6 16.0 0.139 0.0
ALA D:146 D:146 11.0 0.096 S -143.3 26.2 NA NA NA
ALA G:146 G:146 18.0 0.157 S -132.2 8.9 NA NA NA
5d0m 1 P62837 93.2 1e-95 X-RAY
 2015-12-09 ALA A:151 A:146 11.0 0.096 -126.1 5.7 11.0 0.096 0.0 HOH
 2.788
 O
 O
5ulf 1 P62837 93.2 1e-95 X-RAY
 2017-06-07 ALA A:151 A:146 3.0 0.026 -108.3 33.9 3.0 0.026 0.0 HOH
 2.935
 O
 O
ALA C:151 C:146 3.0 0.026 -108.3 38.3 NA NA NA
4ii2 3 P46595 83.67 6e-92 X-RAY
 2013-02-13 ALA C:146 C:146 1.0 0.009 S -101.2 17.1 1.0 0.009 0.0 HOH
 4.081
 CB
 O
2ayv 1 ? 81.38 3e-89 X-RAY
 2005-09-20 ALA A:166 A:146 49.0 NA -116.3 360.0 49.0 NA NA HOH
 3.696
 CB
 O
5aie 2 P15731 81.25 6e-89 X-RAY
 2015-04-29 ALA B:157 B:147 14.0 0.122 I -84.6 -8.2 14.0 0.122 0.0
1qcq 1 P15731 81.25 1e-88 X-RAY
 1999-05-17 ALA A:147 A:147 1.0 0.009 -77.5 55.3 1.0 0.009 0.0

AlphaFold DB

Entity Residue Monomer View
ID Entity Uniprot Identity Evalue Name Label Auth ASA rASA SS φ ψ
af-p61077-f1 1 P61077 97.96 2e-108 ALA A:146 A:146 8.0 0.07 -126.8 1.4
af-p62837-f1 1 P62837 96.6 4e-107 ALA A:146 A:146 8.0 0.07 T -127.0 -1.1
af-q9y2x8-f1 1 Q9Y2X8 92.52 1e-103 ALA A:146 A:146 6.0 0.052 T -125.7 -1.3
af-p51668-f1 1 P51668 88.44 2e-99 ALA A:146 A:146 9.0 0.078 T -126.8 -0.4