Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr7 43978084 . G A CCDS5474.1:NM_015983.3:c.79Ggt>Agt_NP_057067.1:p.27G>S 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 GLY A:32 A:27 66.0 0.88 S 96.2 -98.6 66.0 0.88 0.0
GLY B:32 B:27 45.0 0.6 S -82.4 -118.8 45.0 0.6 0.0
3tgd 1 P62837 93.2 6e-104 X-RAY
 2011-08-31 GLY A:32 A:27 48.0 0.64 S -136.2 -119.6 48.0 0.64 0.0 HOH
 2.689
 N
 O
7bol 1 P62837 93.2 9e-104 X-RAY
 2021-03-24 GLY A:28 A:27 59.0 0.787 S 99.1 -159.2 59.0 0.787 0.0 HOH
 2.722
 O
 O
1w4u 1 P51669 93.2 9e-104 NMR
 2004-11-10 GLY A:27 A:27 39.0 0.52 S -84.8 8.8 39.0 0.52 0.0
4a49 2 P62837 93.2 9e-104 X-RAY
 2012-01-25 GLY B:27 B:27 66.0 0.88 T 53.3 -134.1 66.0 0.88 0.0 HOH
 2.675
 O
 O
4a4b 3 P62837 93.2 9e-104 X-RAY
 2012-01-25 GLY C:27 C:27 81.0 1.0 T 60.3 -137.1 81.0 1.0 0.0 HOH
 9.864
 N
 O
4a4c 3 P62837 93.2 9e-104 X-RAY
 2012-01-25 GLY C:27 C:27 67.0 0.893 T 64.7 -138.6 67.0 0.893 0.0
5d1k 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 GLY A:27 A:27 65.0 0.867 T 50.8 -130.0 65.0 0.867 0.0 HOH
 2.752
 N
 O
5d1l 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 GLY A:27 A:27 65.0 0.867 T 51.4 -130.2 65.0 0.867 0.0 HOH
 2.611
 N
 O
5d1m 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 GLY A:27 A:27 66.0 0.88 T 51.0 -126.1 66.0 0.88 0.0 HOH
 2.733
 N
 O
2clw 1 P62837 93.2 1e-103 X-RAY
 2007-06-12 GLY A:45 A:27 59.0 0.787 S 97.9 -137.4 59.0 0.787 0.0 HOH
 2.409
 N
 O
2clw 2 P62837 93.2 1e-103 X-RAY
 2007-06-12 GLY B:45 B:27 54.0 0.72 T 84.4 -142.6 NA NA NA
GLY C:45 C:27 69.0 0.92 T 91.5 -129.7 NA NA NA
GLY D:45 D:27 63.0 0.84 T 88.5 -145.3 NA NA NA
3eb6 2 P62840 93.2 1e-103 X-RAY
 2008-09-09 GLY B:29 B:27 40.0 0.533 S -102.5 -155.3 40.0 0.533 0.0
6m2c 1 P62837 93.2 1e-103 X-RAY
 2021-04-07 GLY A:29 A:27 65.0 0.867 T 74.4 -140.8 65.0 0.867 0.0 HOH
 2.752
 HA2
 O
GLY B:29 B:27 54.0 0.72 S -60.2 117.3 NA NA NA
GLY C:29 C:27 43.0 0.573 S 150.5 163.3 NA NA NA
GLY D:29 D:27 49.0 0.653 S 127.0 167.1 NA NA NA
2esk 1 P62837 93.2 1e-103 X-RAY
 2005-12-06 GLY A:29 A:27 51.0 0.68 S -163.6 -119.8 51.0 0.68 0.0 HOH
 2.778
 O
 O
3l1y 1 P62837 92.52 2e-103 X-RAY
 2010-05-05 GLY A:37 A:27 56.0 0.747 S -138.2 -120.1 56.0 0.747 0.0 HOH
 2.781
 N
 O
3l1z 1 P61077 91.84 4e-103 X-RAY
 2010-05-05 GLY A:37 A:27 46.0 0.613 S 76.3 126.9 46.0 0.613 0.0
2esq 1 P62837 92.52 5e-103 X-RAY
 2005-12-06 GLY A:29 A:27 62.0 0.827 T 69.0 -128.5 62.0 0.827 0.0 HOH
 2.672
 O
 O
2eso 1 P62837 92.52 6e-103 X-RAY
 2005-12-06 GLY A:29 A:27 54.0 0.72 S -162.1 -121.1 54.0 0.72 0.0 HOH
 2.743
 O
 O
2esp 1 P62837 92.52 6e-103 X-RAY
 2005-12-06 GLY A:29 A:27 49.0 0.653 S -158.4 -122.1 49.0 0.653 0.0 HOH
 2.652
 O
 O
5egg 1 P61077 91.84 8e-103 X-RAY
 2016-11-02 GLY A:36 A:27 49.0 0.653 S 166.2 -176.6 49.0 0.653 0.0 HOH
 3.089
 N
 O
3a33 1 P62837 92.52 1e-102 X-RAY
 2009-11-24 GLY A:30 A:27 47.0 0.627 S -144.9 -121.1 47.0 0.627 0.0 HOH
 2.705
 O
 O
1x23 1 P61077 91.84 1e-102 X-RAY
 2005-05-03 GLY A:35 A:27 80.0 1.0 T 62.8 31.6 80.0 1.0 0.0 HOH
 3.640
 N
 O
GLY B:35 B:27 61.0 0.813 T 50.4 -134.3 NA NA NA
GLY C:35 C:27 50.0 0.667 S -133.5 -138.8 NA NA NA
GLY D:35 D:27 80.0 1.0 T 77.3 -148.1 NA NA NA
4ldt 3 P62837 92.52 2e-102 X-RAY
 2013-08-14 GLY C:28 C:27 51.0 0.68 S -156.0 -149.2 51.0 0.68 0.0 HOH
 2.660
 N
 O
4wz3 1 P62837 92.52 2e-102 X-RAY
 2015-01-07 GLY A:28 A:27 34.0 0.453 S -172.3 168.3 34.0 0.453 0.0 HOH
 4.498
 CA
 O
6hpr 3 P62837 92.52 3e-102 X-RAY
 2018-12-12 GLY C:27 C:27 74.0 0.987 T 59.6 -138.0 74.0 0.987 0.0 HOH
 2.417
 N
 O
4ddg 1 P62837,Q96FW1 92.52 4e-102 X-RAY
 2012-02-22 GLY A:29 A:27 73.0 0.973 T 53.9 -123.2 18.0 0.24 0.733 B:P62837+Q96FW1:0.733
GLY B:29 B:27 71.0 0.947 T 53.9 -123.2 23.0 0.307 0.64 C:P62837+Q96FW1:0.64
GLY C:29 C:27 71.0 0.947 T 53.9 -123.2 7.0 0.093 0.854 A:P62837+Q96FW1:0.853
GLY J:29 J:27 73.0 0.973 T 53.8 -123.2 NA NA NA
GLY K:29 K:27 72.0 0.96 T 54.0 -123.2 NA NA NA
GLY L:29 L:27 71.0 0.947 T 53.9 -123.2 NA NA NA
4ddi 1 P62837,Q96FW1 92.52 4e-102 X-RAY
 2012-02-22 GLY A:29 A:27 72.0 0.96 T 51.6 -125.1 12.0 0.16 0.8 B:P62837+Q96FW1:0.8
GLY B:29 B:27 72.0 0.96 T 51.7 -125.1 18.0 0.24 0.72 C:P62837+Q96FW1:0.72
GLY C:29 C:27 72.0 0.96 T 51.8 -125.1 16.0 0.213 0.747 A:P62837+Q96FW1:0.747
5zbu 1 P62837 92.52 4e-102 X-RAY
 2019-02-27 GLY A:28 C:27 48.0 0.64 S -129.1 -104.8 48.0 0.64 0.0
GLY B:28 B:27 65.0 0.867 T 68.4 -108.8 NA NA NA
4s3o 1 P61077 91.78 5e-102 X-RAY
 2015-07-15 GLY A:28 A:27 48.0 0.64 S -139.3 -117.9 NA NA NA
GLY B:28 D:27 76.0 1.0 T 46.8 53.8 76.0 1.0 0.0
3rpg 1 P61077 91.78 5e-102 X-RAY
 2011-08-17 GLY A:29 A:27 53.0 0.707 S -175.2 -114.6 53.0 0.707 0.0 HOH
 2.746
 N
 O
6cp0 2 P61077 91.16 6e-102 X-RAY
 2018-08-01 GLY B:29 B:27 60.0 0.8 S 69.4 -170.2 60.0 0.8 0.0
3ugb 1 P61077 91.16 7e-102 X-RAY
 2012-05-16 GLY A:27 A:27 48.0 0.64 S -133.1 -119.8 48.0 0.64 0.0 HOH
 2.833
 N
 O
4bvu 2 P61077 91.16 7e-102 X-RAY
 2014-01-29 GLY B:27 B:27 52.0 0.693 S -111.5 -146.5 52.0 0.693 0.0 HOH
 6.144
 C
 O
1z2u 1 P35129 92.52 8e-102 X-RAY
 2005-03-22 GLY A:30 A:27 64.0 0.853 T 56.9 -134.4 64.0 0.853 0.0 UNX
UNX
UNX
UNX
HOH
 4.557
3.659
5.891
8.710
2.902
 N
CA
N
N
N
 UNK
UNK
UNK
UNK
O
5ifr 1 P61077 91.78 8e-102 X-RAY
 2016-05-11 GLY A:31 A:27 48.0 0.64 S -120.7 -117.0 48.0 0.64 0.0 HOH
 2.734
 N
 O
7lyb 7 P61077 91.78 8e-102 EM
 2021-07-28 GLY J:45 P:27 52.0 0.693 S 133.0 -116.5 52.0 0.693 0.0
5mnj 1 P62837 91.84 2e-101 X-RAY
 2017-05-31 GLY A:27 A:27 72.0 0.96 T 55.2 -128.4 72.0 0.96 0.0
GLY E:27 E:27 54.0 0.72 S -103.5 -144.6 NA NA NA
5vzw 1 P62837 91.84 2e-101 X-RAY
 2017-08-09 GLY A:27 A:27 72.0 0.96 T 73.8 -147.4 72.0 0.96 0.0
GLY E:27 B:27 70.0 0.933 T 73.6 -147.2 70.0 0.933 0.0
7ahz 2 Q28EY6 91.84 2e-101 X-RAY
 2021-01-20 GLY B:27 BBB:27 61.0 0.813 T 56.6 -136.9 NA NA NA
GLY E:27 EEE:27 61.0 0.813 T 58.6 -137.6 NA NA NA
GLY H:27 HHH:27 62.0 0.827 T 56.7 -136.6 NA NA NA
GLY K:27 KKK:27 47.0 0.627 S -140.7 -112.6 NA NA NA
7ai0 2 P62837 91.84 2e-101 X-RAY
 2021-01-20 GLY B:27 BBB:27 50.0 0.667 S -136.7 -114.4 NA NA NA
GLY E:27 EEE:27 66.0 0.88 T 50.5 -135.4 NA NA NA
7ai1 2 P62837 91.84 2e-101 X-RAY
 2021-01-20 GLY B:27 BBB:27 43.0 0.573 S -145.4 -99.2 NA NA NA
GLY E:27 EEE:27 74.0 0.987 T 52.2 -115.3 NA NA NA
3oj4 1 P51668 91.84 2e-101 X-RAY
 2010-12-08 GLY A:33 A:27 71.0 0.947 T 69.0 -139.8 8.0 0.107 0.84 C:P21580:0.84
GLY D:33 D:27 74.0 0.987 T 69.0 -139.9 NA NA NA
3ptf 1 P51668 91.84 2e-101 X-RAY
 2011-05-11 GLY A:33 A:27 51.0 0.68 S -155.9 -109.0 51.0 0.68 0.0
GLY B:33 B:27 52.0 0.693 S -157.8 -110.3 NA NA NA
4r8p 8 Q99496,P61077 91.78 2e-101 X-RAY
 2014-11-05 GLY L:148 L:227 47.0 0.627 S -135.6 -136.3 47.0 0.627 0.0
GLY N:148 N:227 49.0 0.653 S -169.6 -124.1 49.0 0.653 0.0
4v3l 1 P62837 92.47 2e-101 X-RAY
 2015-04-08 GLY A:26 A:27 72.0 0.96 T 54.8 36.3 72.0 0.96 0.0 HOH
 2.814
 N
 O
2yho 2 P51668 91.84 3e-101 X-RAY
 2011-06-29 GLY B:29 B:27 73.0 0.973 S 75.6 -149.9 73.0 0.973 0.0 HOH
 2.555
 O
 O
GLY D:29 D:27 63.0 0.84 T 60.6 -135.0 NA NA NA
GLY F:29 F:27 64.0 0.853 T 64.8 -135.3 NA NA NA
GLY H:29 H:27 68.0 0.907 S 86.6 -153.1 NA NA NA
6d4p 1 P51668 91.84 3e-101 X-RAY
 2019-07-17 GLY A:29 A:27 56.0 0.747 S -127.1 -122.5 54.0 0.72 0.027 B:Q59EM9:0.027
 HOH
 1.651
 H
 O
4qpl 2 P51668 91.84 3e-101 X-RAY
 2014-10-15 GLY B:34 B:27 61.0 0.813 T 61.3 -133.8 61.0 0.813 0.0 HOH
 3.851
 CA
 O
GLY D:34 D:27 67.0 0.893 T 54.5 -143.1 NA NA NA
2c4p 1 P51668 91.84 3e-101 X-RAY
 2006-11-22 GLY A:45 A:27 61.0 0.813 T 66.1 -139.5 61.0 0.813 0.0 HOH
 5.047
 O
 O
GLY B:45 B:27 57.0 0.76 T 69.8 -154.9 NA NA NA
4auq 1 P62837 91.16 8e-101 X-RAY
 2012-08-15 GLY A:27 A:27 47.0 0.627 S -99.0 -141.3 47.0 0.627 0.0 HOH
 3.433
 CA
 O
GLY D:27 D:27 48.0 0.64 S -100.3 -143.1 48.0 0.64 0.0 HOH
 2.465
 N
 O
3zni 3 P62837 91.78 1e-100 X-RAY
 2013-07-10 GLY C:26 C:27 65.0 0.867 T 70.5 -128.5 65.0 0.867 0.0 HOH
 6.334
 N
 O
GLY G:26 G:27 63.0 0.84 T 64.1 -127.3 NA NA NA
GLY K:26 K:27 73.0 0.973 T 60.7 -126.3 NA NA NA
GLY O:26 O:27 74.0 0.987 T 63.7 -128.8 NA NA NA
4v3k 1 P62837 91.78 1e-100 X-RAY
 2015-04-08 GLY A:26 A:27 60.0 0.8 S -107.6 -154.0 NA NA NA
GLY D:26 D:27 45.0 0.6 S -102.8 -142.4 45.0 0.6 0.0 HOH
 2.447
 N
 O
6sqo 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 GLY B:26 B:27 69.0 0.92 T 62.4 -139.4 69.0 0.92 0.0 HOH
 4.088
 CA
 O
GLY E:26 E:27 62.0 0.827 T 56.7 -137.5 62.0 0.827 0.0 HOH
 2.444
 N
 O
6sqr 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 GLY B:26 B:27 50.0 0.667 S -98.1 -139.3 10.0 0.133 0.534 K:P62837:0.533
 HOH
 3.059
 N
 O
GLY E:26 E:27 74.0 0.987 T 56.5 -112.5 74.0 0.987 0.0 HOH
 8.736
 N
 O
GLY H:26 H:27 62.0 0.827 T 70.8 -119.8 62.0 0.827 0.0
GLY K:26 K:27 48.0 0.64 S -123.5 -109.9 48.0 0.64 0.0 HOH
 3.464
 O
 O
6sqs 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 GLY B:26 B:27 57.0 0.76 S -147.6 -111.2 57.0 0.76 0.0 HOH
 9.835
 N
 O
GLY E:26 E:27 62.0 0.827 T 62.9 -120.0 62.0 0.827 0.0 HOH
 7.729
 O
 O
5edv 2 P62837 91.78 2e-100 X-RAY
 2016-01-20 GLY C:29 C:27 57.0 0.76 S -138.1 -120.8 57.0 0.76 0.0
GLY D:29 D:27 56.0 0.747 S -138.6 -121.2 NA NA NA
GLY I:29 I:27 56.0 0.747 S -139.7 -122.1 NA NA NA
6ttu 6 P62837 91.16 4e-100 EM
 2020-02-12 GLY F:27 D:27 50.0 0.667 S -138.2 -124.5 48.0 0.64 0.027 A:Q9Y297:0.027
3jvz 1 P62837 91.1 6e-100 X-RAY
 2010-01-12 GLY A:26 A:27 61.0 0.813 S 89.0 -152.2 61.0 0.813 0.0
GLY B:26 B:27 70.0 0.933 S 75.3 -101.1 NA NA NA
3jw0 1 P62837 91.1 6e-100 X-RAY
 2010-01-12 GLY A:26 A:27 64.0 0.853 S 74.9 -167.6 64.0 0.853 0.0
GLY B:26 B:27 61.0 0.813 T 73.5 -119.3 NA NA NA
5tut 1 P51668 91.16 7e-100 X-RAY
 2017-11-08 GLY A:30 A:27 47.0 0.627 S -142.2 -120.3 47.0 0.627 0.0
7jzv 1 A0A386IN42,P61077 91.1 8e-100 EM
 2021-02-17 GLY A:138 A:227 69.0 0.92 S 120.0 -1.6 69.0 0.92 0.0
4ap4 2 P51668 90.48 3e-99 X-RAY
 2012-07-25 GLY B:33 B:27 58.0 0.773 T 69.7 -155.0 58.0 0.773 0.0 HOH
 4.875
 C
 O
GLY D:33 E:27 58.0 0.773 T 69.7 -154.4 58.0 0.773 0.0 HOH
 9.770
 N
 O
5fer 2 P51668 90.48 7e-99 X-RAY
 2016-05-18 GLY B:30 B:27 49.0 0.653 S -90.4 -162.2 49.0 0.653 0.0 HOH
 2.563
 N
 O
GLY E:30 E:27 49.0 0.653 S -134.1 -117.8 49.0 0.653 0.0
6w7z 1 P62837 90.48 1e-93 X-RAY
 2020-05-20 GLY A:32 A:27 45.0 0.6 S -121.5 -121.9 45.0 0.6 0.0 HOH
 2.598
 N
 O
5d0k 1 P62837 90.48 3e-93 X-RAY
 2015-12-09 GLY A:32 A:27 68.0 0.907 T 60.2 -126.8 68.0 0.907 0.0
GLY C:32 D:27 64.0 0.853 T 63.7 -138.9 NA NA NA
GLY E:32 G:27 68.0 0.907 T 57.4 -126.9 NA NA NA
GLY G:32 J:27 64.0 0.853 T 58.2 -127.7 NA NA NA
5ulh 1 P62837 90.48 3e-93 X-RAY
 2017-06-07 GLY A:32 A:27 67.0 0.893 T 46.9 -121.8 67.0 0.893 0.0 HOH
 2.739
 N
 O
5ulk 1 P62837 90.48 3e-93 X-RAY
 2017-06-07 GLY A:32 A:27 41.0 0.547 S -136.7 -121.5 40.0 0.533 0.014 B:P0CG47:0.013
6w9d 1 P62837 89.8 1e-92 X-RAY
 2020-05-20 GLY A:27 A:27 46.0 0.613 S -115.8 -132.3 46.0 0.613 0.0
GLY D:27 D:27 46.0 0.613 S -120.1 -127.9 NA NA NA
GLY G:27 G:27 45.0 0.6 S -120.4 -132.1 NA NA NA
5d0m 1 P62837 89.8 2e-92 X-RAY
 2015-12-09 GLY A:32 A:27 67.0 0.893 T 60.8 -108.7 67.0 0.893 0.0
5ulf 1 P62837 89.8 2e-92 X-RAY
 2017-06-07 GLY A:32 A:27 50.0 0.667 S 170.3 -165.4 50.0 0.667 0.0 HOH
 2.510
 O
 O
GLY C:32 C:27 49.0 0.653 S 169.7 -168.3 NA NA NA
6t7f 2 P61077 89.04 6e-92 X-RAY
 2020-08-05 GLY B:30 B:27 52.0 0.693 S -138.3 -143.9 52.0 0.693 0.0 HOH
 3.876
 CA
 O
4ii2 3 P46595 82.31 6e-91 X-RAY
 2013-02-13 GLY C:27 C:27 74.0 0.987 T 54.0 35.5 61.0 0.813 0.174 A:O94609:0.173
 HOH
 9.256
 O
 O
5aie 2 P15731 81.25 1e-89 X-RAY
 2015-04-29 GLY B:38 B:28 73.0 0.973 T 72.5 -111.3 73.0 0.973 0.0
1qcq 1 P15731 81.25 2e-89 X-RAY
 1999-05-17 GLY A:28 A:28 61.0 0.813 T 77.7 -139.9 61.0 0.813 0.0
2ayv 1 ? 81.38 3e-89 X-RAY
 2005-09-20 GLY A:47 A:27 70.0 0.933 S 91.0 -157.7 70.0 0.933 0.0
4x57 1 P35131 80.27 3e-89 X-RAY
 2016-01-20 ALA A:58 A:27 78.0 0.678 S -136.0 -109.3 47.0 0.409 0.269 B:Q9SW27:0.27
ALA C:58 C:27 72.0 0.626 S -130.6 -110.1 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 GLY A:27 A:27 62.0 0.827 T 63.9 -136.4
af-p62837-f1 1 P62837 93.2 4e-104 GLY A:27 A:27 65.0 0.867 T 63.3 -135.5
af-p61077-f1 1 P61077 91.84 2e-103 GLY A:27 A:27 66.0 0.88 T 62.9 -134.4
af-p51668-f1 1 P51668 91.84 1e-101 GLY A:27 A:27 65.0 0.867 T 64.1 -137.1