Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr7 43992270 . G A CCDS5474.1:NM_015983.3:c.420gaG>gaA_NP_057067.1:p.140E>E 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 GLU A:145 A:140 79.0 0.416 H -54.8 -47.8 79.0 0.416 0.0
GLU B:145 B:140 81.0 0.426 H -67.4 -51.8 81.0 0.426 0.0
3tgd 1 P62837 93.2 6e-104 X-RAY
 2011-08-31 GLU A:145 A:140 102.0 0.537 H -62.5 -43.4 102.0 0.537 0.0 HOH
 2.626
 OE2
 O
7bol 1 P62837 93.2 9e-104 X-RAY
 2021-03-24 GLU A:141 A:140 78.0 0.411 H -60.7 -43.6 78.0 0.411 0.0 HOH
 2.541
 OE2
 O
1w4u 1 P51669 93.2 9e-104 NMR
 2004-11-10 GLU A:140 A:140 56.0 0.295 H -67.1 -42.6 56.0 0.295 0.0
4a49 2 P62837 93.2 9e-104 X-RAY
 2012-01-25 GLU B:140 B:140 92.0 0.484 H -58.9 -41.5 92.0 0.484 0.0 HOH
 3.441
 OE2
 O
4a4b 3 P62837 93.2 9e-104 X-RAY
 2012-01-25 GLU C:140 C:140 114.0 0.6 H -63.8 -38.3 114.0 0.6 0.0
4a4c 3 P62837 93.2 9e-104 X-RAY
 2012-01-25 GLU C:140 C:140 112.0 0.589 H -68.6 -45.9 112.0 0.589 0.0
5d1k 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 GLU A:140 A:140 89.0 0.468 H -62.2 -47.4 89.0 0.468 0.0 EDO
PEG
OXL
HOH
 5.682
8.816
5.387
2.520
 OE1
O
CB
OE1
 O1
O1
O4
O
5d1l 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 GLU A:140 A:140 83.0 0.437 H -59.8 -43.0 83.0 0.437 0.0 PEG
OXL
HOH
 8.387
4.622
2.501
 C
O
OE1
 O1
O4
O
5d1m 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 GLU A:140 A:140 87.0 0.458 H -58.6 -46.3 87.0 0.458 0.0 HOH
 2.876
 O
 O
2clw 1 P62837 93.2 1e-103 X-RAY
 2007-06-12 GLU A:158 A:140 101.0 0.532 H -60.1 -47.6 101.0 0.532 0.0 SO4
HOH
 5.112
2.406
 OE2
OE1
 O3
O
2clw 2 P62837 93.2 1e-103 X-RAY
 2007-06-12 GLU B:158 B:140 96.0 0.505 H -71.2 -43.8 NA NA NA
GLU C:158 C:140 81.0 0.426 H -68.4 -45.8 NA NA NA
GLU D:158 D:140 84.0 0.442 H -63.0 -54.0 NA NA NA
3eb6 2 P62840 93.2 1e-103 X-RAY
 2008-09-09 GLU B:142 B:140 89.0 0.468 H -59.6 -44.9 89.0 0.468 0.0
6m2c 1 P62837 93.2 1e-103 X-RAY
 2021-04-07 GLU A:142 A:140 95.0 0.5 H -64.8 -44.1 95.0 0.5 0.0
GLU B:142 B:140 75.0 0.395 H -64.8 -39.0 NA NA NA
GLU C:142 C:140 78.0 0.411 H -62.7 -41.1 NA NA NA
GLU D:142 D:140 93.0 0.489 H -65.6 -38.5 NA NA NA
2esk 1 P62837 93.2 1e-103 X-RAY
 2005-12-06 GLU A:142 A:140 79.0 0.416 H -62.3 -43.0 79.0 0.416 0.0 HOH
 2.537
 OE1
 O
3l1y 1 P62837 92.52 2e-103 X-RAY
 2010-05-05 GLU A:150 A:140 90.0 0.474 H -54.9 -50.2 90.0 0.474 0.0 HOH
 2.762
 OE2
 O
3l1z 1 P61077 91.84 4e-103 X-RAY
 2010-05-05 GLU A:150 A:140 97.0 0.511 H -55.7 -35.7 97.0 0.511 0.0 HOH
 9.984
 O
 O
2esq 1 P62837 92.52 5e-103 X-RAY
 2005-12-06 GLU A:142 A:140 91.0 0.479 H -60.3 -41.5 91.0 0.479 0.0 HOH
 2.312
 OE1
 O
2eso 1 P62837 92.52 6e-103 X-RAY
 2005-12-06 GLU A:142 A:140 96.0 0.505 H -61.6 -41.8 96.0 0.505 0.0 HOH
 2.261
 OE1
 O
2esp 1 P62837 92.52 6e-103 X-RAY
 2005-12-06 GLU A:142 A:140 80.0 0.421 H -64.7 -41.8 80.0 0.421 0.0 HOH
 2.333
 OE1
 O
5egg 1 P61077 91.84 8e-103 X-RAY
 2016-11-02 GLU A:149 A:140 109.0 0.574 H -54.7 -49.4 109.0 0.574 0.0 HOH
 2.386
 OE2
 O
3a33 1 P62837 92.52 1e-102 X-RAY
 2009-11-24 GLU A:143 A:140 80.0 0.421 H -66.8 -42.9 80.0 0.421 0.0 HOH
 6.018
 C
 O
1x23 1 P61077 91.84 1e-102 X-RAY
 2005-05-03 GLU A:148 A:140 83.0 0.437 H -63.7 -49.1 83.0 0.437 0.0 HOH
 2.841
 OE1
 O
GLU B:148 B:140 114.0 0.6 H -72.3 -36.3 NA NA NA
GLU C:148 C:140 95.0 0.5 H -66.4 -43.2 NA NA NA
GLU D:148 D:140 93.0 0.489 H -67.8 -48.3 NA NA NA
4ldt 3 P62837 92.52 2e-102 X-RAY
 2013-08-14 GLU C:141 C:140 97.0 0.511 H -67.2 -44.6 97.0 0.511 0.0 HOH
 2.412
 OE2
 O
4wz3 1 P62837 92.52 2e-102 X-RAY
 2015-01-07 GLU A:141 A:140 101.0 0.532 H -76.4 -37.6 101.0 0.532 0.0 HOH
 6.126
 C
 O
6hpr 3 P62837 92.52 3e-102 X-RAY
 2018-12-12 GLU C:140 C:140 97.0 0.511 H -62.7 -44.3 97.0 0.511 0.0 HOH
 2.607
 OE2
 O
4ddg 1 P62837,Q96FW1 92.52 4e-102 X-RAY
 2012-02-22 GLU A:142 A:140 91.0 0.479 H -63.7 -42.8 91.0 0.479 0.0
GLU B:142 B:140 92.0 0.484 H -63.7 -42.8 92.0 0.484 0.0
GLU C:142 C:140 92.0 0.484 H -63.7 -42.8 92.0 0.484 0.0
GLU J:142 J:140 92.0 0.484 H -63.8 -42.8 NA NA NA
GLU K:142 K:140 91.0 0.479 H -63.8 -42.8 NA NA NA
GLU L:142 L:140 91.0 0.479 H -63.8 -42.9 NA NA NA
4ddi 1 P62837,Q96FW1 92.52 4e-102 X-RAY
 2012-02-22 GLU A:142 A:140 63.0 0.332 H -79.0 -34.0 63.0 0.332 0.0
GLU B:142 B:140 63.0 0.332 H -79.0 -34.1 63.0 0.332 0.0
GLU C:142 C:140 63.0 0.332 H -79.0 -34.1 63.0 0.332 0.0
5zbu 1 P62837 92.52 4e-102 X-RAY
 2019-02-27 GLU A:141 C:140 86.0 0.453 H -54.1 -53.4 86.0 0.453 0.0
GLU B:141 B:140 85.0 0.447 H -53.5 -58.1 NA NA NA
4s3o 1 P61077 91.78 5e-102 X-RAY
 2015-07-15 GLU A:141 A:140 122.0 0.642 H -68.6 -46.3 NA NA NA
GLU B:141 D:140 95.0 0.5 H -57.2 -48.0 95.0 0.5 0.0 HOH
 5.908
 C
 O
3rpg 1 P61077 91.78 5e-102 X-RAY
 2011-08-17 GLU A:142 A:140 78.0 0.411 H -60.3 -46.6 78.0 0.411 0.0 HOH
 5.600
 C
 O
6cp0 2 P61077 91.16 6e-102 X-RAY
 2018-08-01 GLU B:142 B:140 106.0 0.558 H -59.9 -38.2 106.0 0.558 0.0
3ugb 1 P61077 91.16 7e-102 X-RAY
 2012-05-16 GLU A:140 A:140 97.0 0.511 H -60.2 -40.0 97.0 0.511 0.0 HOH
 2.369
 OE1
 O
4bvu 2 P61077 91.16 7e-102 X-RAY
 2014-01-29 GLU B:140 B:140 78.0 0.411 H -62.7 -41.3 78.0 0.411 0.0 HOH
 5.878
 C
 O
1z2u 1 P35129 92.52 8e-102 X-RAY
 2005-03-22 GLU A:143 A:140 109.0 0.574 H -62.9 -45.4 109.0 0.574 0.0 CL
CL
HOH
 6.996
9.879
2.595
 O
OE1
OE1
 CL
CL
O
5ifr 1 P61077 91.78 8e-102 X-RAY
 2016-05-11 GLU A:144 A:140 103.0 0.542 H -64.4 -45.0 103.0 0.542 0.0 GOL
HOH
 5.560
3.492
 OE1
OE2
 C1
O
7lyb 7 P61077 91.78 8e-102 EM
 2021-07-28 GLU J:158 P:140 106.0 0.558 H -62.1 -44.3 106.0 0.558 0.0
5mnj 1 P62837 91.84 2e-101 X-RAY
 2017-05-31 GLU A:140 A:140 90.0 0.474 H -68.3 -47.6 90.0 0.474 0.0 HOH
 5.906
 C
 O
GLU E:140 E:140 95.0 0.5 H -61.0 -45.0 NA NA NA
5vzw 1 P62837 91.84 2e-101 X-RAY
 2017-08-09 GLU A:140 A:140 86.0 0.453 H -60.2 -50.1 86.0 0.453 0.0 HOH
 5.921
 C
 O
GLU E:140 B:140 86.0 0.453 H -60.3 -50.3 86.0 0.453 0.0
7ahz 2 Q28EY6 91.84 2e-101 X-RAY
 2021-01-20 GLU B:140 BBB:140 89.0 0.468 H -59.6 -49.8 NA NA NA
GLU E:140 EEE:140 99.0 0.521 H -58.8 -49.8 NA NA NA
GLU H:140 HHH:140 98.0 0.516 H -59.2 -48.9 NA NA NA
GLU K:140 KKK:140 55.0 NA H -59.9 -49.3 NA NA NA
7ai0 2 P62837 91.84 2e-101 X-RAY
 2021-01-20 GLU B:140 BBB:140 77.0 0.405 H -58.6 -45.2 NA NA NA
GLU E:140 EEE:140 109.0 0.574 H -60.7 -44.7 NA NA NA
7ai1 2 P62837 91.84 2e-101 X-RAY
 2021-01-20 GLU B:140 BBB:140 95.0 0.5 H -60.0 -46.5 NA NA NA
GLU E:140 EEE:140 105.0 0.553 H -59.0 -48.7 NA NA NA
3oj4 1 P51668 91.84 2e-101 X-RAY
 2010-12-08 GLU A:146 A:140 75.0 0.395 H -56.8 -47.2 75.0 0.395 0.0
GLU D:146 D:140 71.0 0.374 H -56.6 -47.5 NA NA NA
3ptf 1 P51668 91.84 2e-101 X-RAY
 2011-05-11 GLU A:146 A:140 100.0 0.526 H -55.9 -44.6 100.0 0.526 0.0 HOH
 5.263
 OE1
 O
GLU B:146 B:140 102.0 0.537 H -60.8 -48.8 NA NA NA
4r8p 8 Q99496,P61077 91.78 2e-101 X-RAY
 2014-11-05 GLU L:261 L:340 66.0 NA T -117.7 -5.1 66.0 NA NA
GLU N:261 N:340 95.0 0.5 H -68.8 -50.1 95.0 0.5 0.0
4v3l 1 P62837 92.47 2e-101 X-RAY
 2015-04-08 GLU A:139 A:140 110.0 0.579 H -62.5 -41.6 110.0 0.579 0.0 HOH
 2.736
 O
 O
2yho 2 P51668 91.84 3e-101 X-RAY
 2011-06-29 GLU B:142 B:140 88.0 0.463 H -61.8 -44.7 88.0 0.463 0.0 HOH
 5.816
 C
 O
GLU D:142 D:140 75.0 0.395 H -56.8 -46.9 NA NA NA
GLU F:142 F:140 93.0 0.489 H -59.1 -42.3 NA NA NA
GLU H:142 H:140 77.0 0.405 H -55.9 -53.1 NA NA NA
6d4p 1 P51668 91.84 3e-101 X-RAY
 2019-07-17 GLU A:142 A:140 118.0 0.621 H -66.2 -44.8 118.0 0.621 0.0 HOH
 5.726
 C
 O
4qpl 2 P51668 91.84 3e-101 X-RAY
 2014-10-15 GLU B:147 B:140 98.0 0.516 H -58.7 -44.3 98.0 0.516 0.0 HOH
 2.531
 OE1
 O
GLU D:147 D:140 82.0 0.432 H -58.2 -47.0 NA NA NA
2c4p 1 P51668 91.84 3e-101 X-RAY
 2006-11-22 GLU A:158 A:140 107.0 0.563 H -58.7 -38.4 107.0 0.563 0.0 HOH
 4.333
 OE1
 O
GLU B:158 B:140 102.0 0.537 H -64.1 -22.1 NA NA NA
4auq 1 P62837 91.16 8e-101 X-RAY
 2012-08-15 GLU A:140 A:140 104.0 0.547 H -59.3 -46.4 104.0 0.547 0.0 HOH
 5.904
 O
 O
GLU D:140 D:140 90.0 0.474 H -57.2 -44.3 90.0 0.474 0.0 HOH
 6.000
 C
 O
3zni 3 P62837 91.78 1e-100 X-RAY
 2013-07-10 GLU C:139 C:140 100.0 0.526 H -55.6 -45.7 100.0 0.526 0.0 HOH
 2.678
 O
 O
GLU G:139 G:140 101.0 0.532 H -61.9 -50.0 NA NA NA
GLU K:139 K:140 101.0 0.532 H -66.5 -44.3 NA NA NA
GLU O:139 O:140 94.0 0.495 H -59.4 -42.4 NA NA NA
4v3k 1 P62837 91.78 1e-100 X-RAY
 2015-04-08 GLU A:139 A:140 128.0 0.674 H -66.4 -39.6 NA NA NA
GLU D:139 D:140 101.0 0.532 H -60.5 -44.5 101.0 0.532 0.0 HOH
 2.492
 OE1
 O
6sqo 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 GLU B:139 B:140 112.0 0.589 H -58.4 -44.6 112.0 0.589 0.0 NO3
HOH
 3.330
2.599
 OE2
OE1
 O1
O
GLU E:139 E:140 60.0 0.316 H -61.1 -42.7 60.0 0.316 0.0 HOH
 2.611
 OE1
 O
6sqr 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 GLU B:139 B:140 111.0 0.584 H -62.5 -39.7 111.0 0.584 0.0 HOH
 5.932
 C
 O
GLU E:139 E:140 93.0 0.489 H -66.0 -48.6 93.0 0.489 0.0 HOH
 7.918
 O
 O
GLU H:139 H:140 94.0 0.495 H -61.2 -49.6 94.0 0.495 0.0 HOH
 6.046
 C
 O
GLU K:139 K:140 92.0 0.484 H -61.9 -44.2 92.0 0.484 0.0 HOH
 2.710
 OE1
 O
6sqs 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 GLU B:139 B:140 85.0 0.447 H -64.6 -47.4 85.0 0.447 0.0 HOH
 5.949
 C
 O
GLU E:139 E:140 107.0 0.563 H -65.4 -45.9 107.0 0.563 0.0 HOH
 2.621
 OE1
 O
5edv 2 P62837 91.78 2e-100 X-RAY
 2016-01-20 GLU C:142 C:140 81.0 0.426 H -62.7 -43.2 81.0 0.426 0.0
GLU D:142 D:140 76.0 0.4 H -62.6 -43.3 NA NA NA
GLU I:142 I:140 87.0 0.458 H -62.7 -43.3 NA NA NA
6ttu 6 P62837 91.16 4e-100 EM
 2020-02-12 GLU F:140 D:140 110.0 0.579 H -61.2 -45.0 110.0 0.579 0.0
3jvz 1 P62837 91.1 6e-100 X-RAY
 2010-01-12 GLU A:139 A:140 92.0 0.484 H -74.2 -41.9 92.0 0.484 0.0
GLU B:139 B:140 100.0 0.526 H -71.2 -47.4 NA NA NA
3jw0 1 P62837 91.1 6e-100 X-RAY
 2010-01-12 GLU A:139 A:140 108.0 0.568 H -62.4 -33.4 108.0 0.568 0.0
GLU B:139 B:140 91.0 0.479 H -62.3 -35.1 NA NA NA
5tut 1 P51668 91.16 7e-100 X-RAY
 2017-11-08 GLU A:143 A:140 74.0 0.389 H -57.4 -53.0 74.0 0.389 0.0
7jzv 1 A0A386IN42,P61077 91.1 8e-100 EM
 2021-02-17 GLU A:251 A:340 130.0 0.684 H -63.7 -40.4 130.0 0.684 0.0
4ap4 2 P51668 90.48 3e-99 X-RAY
 2012-07-25 GLU B:146 B:140 98.0 0.516 H -73.7 -34.0 98.0 0.516 0.0 HOH
 2.570
 OE1
 O
GLU D:146 E:140 101.0 0.532 H -73.7 -33.2 101.0 0.532 0.0 HOH
 5.827
 C
 O
5fer 2 P51668 90.48 7e-99 X-RAY
 2016-05-18 GLU B:143 B:140 97.0 0.511 H -69.4 -41.8 97.0 0.511 0.0 HOH
 6.034
 C
 O
GLU E:143 E:140 90.0 0.474 H -65.1 -41.7 90.0 0.474 0.0 HOH
 6.182
 C
 O
6w7z 1 P62837 90.48 1e-93 X-RAY
 2020-05-20 GLU A:145 A:140 99.0 0.521 H -60.9 -45.1 99.0 0.521 0.0 HOH
 2.328
 OE1
 O
5d0k 1 P62837 90.48 3e-93 X-RAY
 2015-12-09 GLU A:145 A:140 78.0 0.411 H -66.9 -42.8 78.0 0.411 0.0
GLU C:145 D:140 80.0 0.421 H -61.1 -45.2 NA NA NA
GLU E:145 G:140 95.0 0.5 H -62.6 -41.8 NA NA NA
GLU G:145 J:140 96.0 0.505 H -62.7 -46.4 NA NA NA
5ulh 1 P62837 90.48 3e-93 X-RAY
 2017-06-07 GLU A:145 A:140 84.0 0.442 H -64.0 -41.4 84.0 0.442 0.0 HOH
 5.888
 C
 O
5ulk 1 P62837 90.48 3e-93 X-RAY
 2017-06-07 GLU A:145 A:140 110.0 0.579 H -62.9 -53.4 110.0 0.579 0.0
6w9d 1 P62837 89.8 1e-92 X-RAY
 2020-05-20 GLU A:140 A:140 97.0 0.511 H -71.5 -31.9 97.0 0.511 0.0
GLU D:140 D:140 98.0 0.516 H -70.5 -33.8 NA NA NA
GLU G:140 G:140 100.0 0.526 H -69.7 -33.8 NA NA NA
5d0m 1 P62837 89.8 2e-92 X-RAY
 2015-12-09 GLU A:145 A:140 85.0 0.447 H -61.5 -48.0 85.0 0.447 0.0 HOH
 2.549
 OE1
 O
5ulf 1 P62837 89.8 2e-92 X-RAY
 2017-06-07 GLU A:145 A:140 112.0 0.589 H -61.2 -46.9 112.0 0.589 0.0 HOH
 6.001
 C
 O
GLU C:145 C:140 114.0 0.6 H -61.0 -47.0 NA NA NA
6t7f 2 P61077 89.04 6e-92 X-RAY
 2020-08-05 GLU B:143 B:140 104.0 0.547 H -58.1 -49.1 104.0 0.547 0.0 HOH
 6.122
 C
 O
4ii2 3 P46595 82.31 6e-91 X-RAY
 2013-02-13 GLU C:140 C:140 70.0 0.368 H -63.3 -44.8 70.0 0.368 0.0 SO4
HOH
 9.411
2.821
 O
OE1
 O2
O
5aie 2 P15731 81.25 1e-89 X-RAY
 2015-04-29 GLU B:151 B:141 119.0 0.626 H -61.9 -42.9 119.0 0.626 0.0
1qcq 1 P15731 81.25 2e-89 X-RAY
 1999-05-17 GLU A:141 A:141 98.0 0.516 H -59.1 -52.1 98.0 0.516 0.0
2ayv 1 ? 81.38 3e-89 X-RAY
 2005-09-20 GLU A:160 A:140 106.0 0.558 H -59.5 -46.3 106.0 0.558 0.0 UNX
HOH
 4.285
5.896
 OE2
C
 UNK
O
4x57 1 P35131 80.27 3e-89 X-RAY
 2016-01-20 ASN A:171 A:140 85.0 0.531 H -58.8 -50.8 85.0 0.531 0.0
ASN C:171 C:140 83.0 0.519 H -60.0 -51.2 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 GLU A:140 A:140 83.0 0.437 H -58.9 -40.3
af-p62837-f1 1 P62837 93.2 4e-104 GLU A:140 A:140 91.0 0.479 H -59.2 -39.9
af-p61077-f1 1 P61077 91.84 2e-103 GLU A:140 A:140 89.0 0.468 H -58.1 -41.3
af-p51668-f1 1 P51668 91.84 1e-101 GLU A:140 A:140 92.0 0.484 H -57.4 -43.6