Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr10 60121266 . C A CCDS7252.1:NM_003338.4:c.100Caa>Aaa_NP_003329.1:p.34Q>K 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 GLN A:40 A:34 103.0 0.572 E -117.0 143.8 36.0 0.2 0.372 B:P0CG47:0.356
C:P21580:0.033
GLN D:40 D:34 102.0 0.567 E -116.3 143.1 NA NA NA
3ptf 1 P51668 100.0 2e-109 X-RAY
 2011-05-11 GLN A:40 A:34 91.0 0.506 E -124.4 155.0 38.0 0.211 0.295 C:P0CG47:0.294
 HOH
 8.108
 N
 O
GLN B:40 B:34 96.0 0.533 E -125.1 156.6 NA NA NA
2yho 2 P51668 100.0 2e-109 X-RAY
 2011-06-29 GLN B:36 B:34 86.0 0.478 E -108.3 142.4 86.0 0.478 0.0 HOH
 2.838
 OE1
 O
GLN D:36 D:34 93.0 0.517 E -113.3 130.8 NA NA NA
GLN F:36 F:34 92.0 0.511 E -114.0 130.8 NA NA NA
GLN H:36 H:34 90.0 0.5 E -101.5 137.3 NA NA NA
6d4p 1 P51668 100.0 2e-109 X-RAY
 2019-07-17 GLN A:36 A:34 93.0 0.517 E -118.8 143.0 51.0 0.283 0.234 B:Q59EM9:0.233
 HOH
 7.197
 H
 O
4qpl 2 P51668 100.0 3e-109 X-RAY
 2014-10-15 GLN B:41 B:34 78.0 0.433 E -107.0 149.2 78.0 0.433 0.0 HOH
 3.419
 C
 O
GLN D:41 D:34 86.0 0.478 E -107.8 141.8 NA NA NA
2c4p 1 P51668 100.0 4e-109 X-RAY
 2006-11-22 GLN A:52 A:34 64.0 0.356 E -145.7 144.3 64.0 0.356 0.0 HOH
 8.058
 NE2
 O
GLN B:52 B:34 94.0 0.522 E -136.8 152.0 NA NA NA
5tut 1 P51668 99.32 6e-108 X-RAY
 2017-11-08 GLN A:37 A:34 90.0 0.5 E -114.4 146.8 90.0 0.5 0.0
4ap4 2 P51668 98.64 2e-107 X-RAY
 2012-07-25 GLN B:40 B:34 103.0 0.572 E -105.6 143.8 103.0 0.572 0.0 HOH
 3.786
 CG
 O
GLN D:40 E:34 105.0 0.583 E -106.8 144.3 105.0 0.583 0.0 HOH
 3.270
 NE2
 O
5fer 2 P51668 98.64 4e-107 X-RAY
 2016-05-18 GLN B:37 B:34 88.0 0.489 E -114.9 126.5 88.0 0.489 0.0 HOH
 5.233
 N
 O
GLN E:37 E:34 73.0 0.406 E -124.5 125.5 73.0 0.406 0.0
2oxq 1 Q6PC58 94.56 3e-103 X-RAY
 2008-02-19 GLN A:39 A:34 61.0 0.339 E -123.1 145.7 61.0 0.339 0.0
GLN B:39 B:34 91.0 0.506 E -133.9 134.6 91.0 0.506 0.0
1z2u 1 P35129 89.12 6e-100 X-RAY
 2005-03-22 GLN A:37 A:34 73.0 0.406 E -117.8 151.7 73.0 0.406 0.0 UNX
UNX
HOH
 9.167
3.696
7.100
 O
O
O
 UNK
UNK
O
3tgd 1 P62837 89.12 1e-99 X-RAY
 2011-08-31 GLN A:39 A:34 93.0 0.517 E -117.3 149.5 93.0 0.517 0.0 HOH
 2.400
 CD
 O
7bol 1 P62837 89.12 1e-99 X-RAY
 2021-03-24 GLN A:35 A:34 99.0 0.55 E -110.0 152.7 99.0 0.55 0.0 HOH
 2.379
 OE1
 O
2esk 1 P62837 89.12 1e-99 X-RAY
 2005-12-06 GLN A:36 A:34 98.0 0.544 E -111.1 157.0 98.0 0.544 0.0 HOH
 7.096
 O
 O
3eb6 2 P62840 89.12 1e-99 X-RAY
 2008-09-09 GLN B:36 B:34 86.0 0.478 E -126.3 125.9 86.0 0.478 0.0
6m2c 1 P62837 89.12 1e-99 X-RAY
 2021-04-07 GLN A:36 A:34 94.0 0.522 E -128.2 137.1 94.0 0.522 0.0 HOH
 9.231
 HE22
 O
GLN B:36 B:34 59.0 0.328 E -126.2 137.2 NA NA NA
GLN C:36 C:34 97.0 0.539 E -129.6 136.9 NA NA NA
GLN D:36 D:34 74.0 0.411 E -128.1 135.6 NA NA NA
1w4u 1 P51669 89.12 2e-99 NMR
 2004-11-10 GLN A:34 A:34 58.0 0.322 E -121.9 118.0 58.0 0.322 0.0
4a49 2 P62837 89.12 2e-99 X-RAY
 2012-01-25 GLN B:34 B:34 93.0 0.517 E -125.3 153.1 93.0 0.517 0.0 HOH
 3.335
 OE1
 O
4a4b 3 P62837 89.12 2e-99 X-RAY
 2012-01-25 GLN C:34 C:34 93.0 0.517 E -108.9 146.6 93.0 0.517 0.0 HOH
 9.906
 N
 O
4a4c 3 P62837 89.12 2e-99 X-RAY
 2012-01-25 GLN C:34 C:34 90.0 0.5 E -102.6 141.0 90.0 0.5 0.0
5d1k 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 GLN A:34 A:34 94.0 0.522 E -112.2 136.0 62.0 0.344 0.178 B:Q96BH1:0.178
 HOH
 2.773
 OE1
 O
5d1l 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 GLN A:34 A:34 94.0 0.522 E -111.1 141.8 59.0 0.328 0.194 B:Q96BH1:0.194
 HOH
 3.368
 O
 O
5d1m 1 P62837 89.12 2e-99 X-RAY
 2015-10-28 GLN A:34 A:34 99.0 0.55 E -112.7 138.9 66.0 0.367 0.183 B:Q96BH1:0.183
 HOH
 2.806
 NE2
 O
2clw 1 P62837 89.12 2e-99 X-RAY
 2007-06-12 GLN A:52 A:34 79.0 0.439 E -137.2 141.8 79.0 0.439 0.0 HOH
 4.505
 CB
 O
2clw 2 P62837 89.12 2e-99 X-RAY
 2007-06-12 GLN B:52 B:34 86.0 0.478 E -129.7 139.8 NA NA NA
GLN C:52 C:34 83.0 0.461 E -134.6 139.7 NA NA NA
GLN D:52 D:34 49.0 0.272 E -134.3 141.3 NA NA NA
3l1y 1 P62837 88.44 3e-99 X-RAY
 2010-05-05 GLN A:44 A:34 93.0 0.517 E -114.6 156.2 93.0 0.517 0.0 HOH
 2.814
 OE1
 O
3l1z 1 P61077 88.44 3e-99 X-RAY
 2010-05-05 GLN A:44 A:34 87.0 0.483 E -116.2 146.6 87.0 0.483 0.0
2esq 1 P62837 88.44 7e-99 X-RAY
 2005-12-06 GLN A:36 A:34 100.0 0.556 E -112.1 151.1 100.0 0.556 0.0 HOH
 3.539
 NE2
 O
5egg 1 P61077 88.44 7e-99 X-RAY
 2016-11-02 GLN A:43 A:34 83.0 0.461 E -103.4 144.8 83.0 0.461 0.0 HOH
 6.023
 N
 O
2eso 1 P62837 88.44 9e-99 X-RAY
 2005-12-06 GLN A:36 A:34 95.0 0.528 E -108.2 150.3 95.0 0.528 0.0 HOH
 8.230
 N
 O
2esp 1 P62837 88.44 9e-99 X-RAY
 2005-12-06 GLN A:36 A:34 98.0 0.544 E -112.0 156.7 98.0 0.544 0.0 HOH
 3.434
 OE1
 O
1x23 1 P61077 88.44 9e-99 X-RAY
 2005-05-03 GLN A:42 A:34 75.0 0.417 E -121.1 145.3 75.0 0.417 0.0 HOH
 2.612
 NE2
 O
GLN B:42 B:34 62.0 0.344 E -120.8 150.9 NA NA NA
GLN C:42 C:34 77.0 0.428 E -112.7 152.9 NA NA NA
GLN D:42 D:34 72.0 0.4 E -122.3 148.3 NA NA NA
3a33 1 P62837 88.44 2e-98 X-RAY
 2009-11-24 GLN A:37 A:34 94.0 0.522 E -117.2 151.5 94.0 0.522 0.0 HOH
 3.923
 CG
 O
4ldt 3 P62837 88.44 3e-98 X-RAY
 2013-08-14 GLN C:35 C:34 89.0 0.494 E -114.3 144.8 89.0 0.494 0.0 HOH
 3.150
 OE1
 O
4wz3 1 P62837 88.44 3e-98 X-RAY
 2015-01-07 GLN A:35 A:34 85.0 0.472 E -140.7 130.5 85.0 0.472 0.0 HOH
 4.826
 O
 O
4s3o 1 P61077 88.36 4e-98 X-RAY
 2015-07-15 GLN A:35 A:34 98.0 0.544 E -116.2 147.3 NA NA NA
GLN B:35 D:34 88.0 0.489 E -111.4 144.2 88.0 0.489 0.0 HOH
 3.082
 OE1
 O
3rpg 1 P61077 88.36 5e-98 X-RAY
 2011-08-17 GLN A:36 A:34 81.0 0.45 E -123.5 154.7 81.0 0.45 0.0 HOH
 4.864
 N
 O
6hpr 3 P62837 88.44 5e-98 X-RAY
 2018-12-12 GLN C:34 C:34 99.0 0.55 E -116.8 148.0 62.0 0.344 0.206 B:P0CG47:0.206
 HOH
 2.325
 OE1
 O
6cp0 2 P61077 87.76 6e-98 X-RAY
 2018-08-01 GLN B:36 B:34 86.0 0.478 E -126.9 138.7 86.0 0.478 0.0
5zbu 1 P62837 88.44 6e-98 X-RAY
 2019-02-27 GLN A:35 C:34 81.0 0.45 E -125.1 129.4 81.0 0.45 0.0
GLN B:35 B:34 98.0 0.544 E -125.1 129.5 NA NA NA
5ifr 1 P61077 88.36 7e-98 X-RAY
 2016-05-11 GLN A:38 A:34 94.0 0.522 E -124.7 135.4 94.0 0.522 0.0 HOH
 5.616
 O
 O
7lyb 7 P61077 88.36 8e-98 EM
 2021-07-28 GLN J:52 P:34 80.0 0.444 E -119.7 127.9 80.0 0.444 0.0
4ddg 1 P62837,Q96FW1 88.44 1e-97 X-RAY
 2012-02-22 GLN A:36 A:34 65.0 0.361 E -117.5 129.4 62.0 0.344 0.017 B:P62837+Q96FW1:0.017
GLN B:36 B:34 64.0 0.356 E -117.6 129.3 62.0 0.344 0.012 C:P62837+Q96FW1:0.011
GLN C:36 C:34 68.0 0.378 E -117.6 129.3 60.0 0.333 0.045 A:P62837+Q96FW1:0.044
GLN J:36 J:34 64.0 0.356 E -117.5 129.3 NA NA NA
GLN K:36 K:34 65.0 0.361 E -117.5 129.3 NA NA NA
GLN L:36 L:34 67.0 0.372 E -117.5 129.3 NA NA NA
4ddi 1 P62837,Q96FW1 88.44 1e-97 X-RAY
 2012-02-22 GLN A:36 A:34 46.0 0.256 E -142.7 138.1 46.0 0.256 0.0
GLN B:36 B:34 46.0 0.256 E -142.7 138.1 46.0 0.256 0.0
GLN C:36 C:34 45.0 0.25 E -142.8 138.2 45.0 0.25 0.0
3ugb 1 P61077 87.76 1e-97 X-RAY
 2012-05-16 GLN A:34 A:34 91.0 0.506 E -123.0 139.1 91.0 0.506 0.0 HOH
 3.435
 CG
 O
4bvu 2 P61077 87.76 1e-97 X-RAY
 2014-01-29 GLN B:34 B:34 84.0 0.467 E -106.2 143.8 84.0 0.467 0.0 HOH
 3.439
 OE1
 O
4r8p 8 Q99496,P61077 88.36 2e-97 X-RAY
 2014-11-05 GLN L:155 L:234 46.0 NA E -117.0 122.2 46.0 NA NA
GLN N:155 N:234 86.0 0.478 E -120.9 139.4 86.0 0.478 0.0
5mnj 1 P62837 87.76 3e-97 X-RAY
 2017-05-31 GLN A:34 A:34 91.0 0.506 E -117.6 144.3 91.0 0.506 0.0 HOH
 8.517
 CA
 O
GLN E:34 E:34 84.0 0.467 E -115.3 148.1 NA NA NA
5vzw 1 P62837 87.76 3e-97 X-RAY
 2017-08-09 GLN A:34 A:34 94.0 0.522 E -109.9 140.3 94.0 0.522 0.0
GLN E:34 B:34 94.0 0.522 E -109.5 140.2 94.0 0.522 0.0
7ahz 2 Q28EY6 87.76 3e-97 X-RAY
 2021-01-20 GLN B:34 BBB:34 110.0 0.611 E -111.7 138.5 NA NA NA
GLN E:34 EEE:34 92.0 0.511 E -111.0 142.4 NA NA NA
GLN H:34 HHH:34 97.0 0.539 E -114.6 142.9 NA NA NA
GLN K:34 KKK:34 113.0 0.628 E -113.8 139.6 NA NA NA
7ai0 2 P62837 87.76 3e-97 X-RAY
 2021-01-20 GLN B:34 BBB:34 90.0 0.5 E -109.5 148.0 NA NA NA
GLN E:34 EEE:34 79.0 0.439 E -113.2 154.1 NA NA NA
7ai1 2 P62837 87.76 3e-97 X-RAY
 2021-01-20 GLN B:34 BBB:34 97.0 0.539 E -109.4 148.2 NA NA NA
GLN E:34 EEE:34 94.0 0.522 E -112.8 149.6 NA NA NA
4v3l 1 P62837 88.36 5e-97 X-RAY
 2015-04-08 GLN A:33 A:34 99.0 0.55 E -117.8 153.4 65.0 0.361 0.189 D:P0CG48:0.189
 HOH
 2.252
 OE1
 O
4auq 1 P62837 87.07 1e-96 X-RAY
 2012-08-15 GLN A:34 A:34 78.0 0.433 E -113.3 147.2 78.0 0.433 0.0 HOH
 4.293
 CG
 O
GLN D:34 D:34 101.0 0.561 E -105.5 146.3 101.0 0.561 0.0 HOH
 3.724
 O
 O
3zni 3 P62837 87.67 2e-96 X-RAY
 2013-07-10 GLN C:33 C:34 94.0 0.522 E -124.6 142.1 94.0 0.522 0.0 HOH
 2.615
 OE1
 O
GLN G:33 G:34 93.0 0.517 E -119.1 142.8 NA NA NA
GLN K:33 K:34 95.0 0.528 E -118.5 144.8 NA NA NA
GLN O:33 O:34 92.0 0.511 E -120.5 140.2 NA NA NA
4v3k 1 P62837 87.67 2e-96 X-RAY
 2015-04-08 GLN A:33 A:34 88.0 0.489 E -101.4 144.8 NA NA NA
GLN D:33 D:34 81.0 0.45 E -115.4 152.9 81.0 0.45 0.0 HOH
 2.676
 OE1
 O
6sqo 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 GLN B:33 B:34 81.0 0.45 E -115.0 154.2 81.0 0.45 0.0 HOH
 2.650
 OE1
 O
GLN E:33 E:34 96.0 0.533 E -114.7 143.6 96.0 0.533 0.0 HOH
 3.046
 O
 O
6sqr 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 GLN B:33 B:34 99.0 0.55 E -107.5 143.4 86.0 0.478 0.072 K:P62837:0.072
 HOH
 6.933
 O
 O
GLN E:33 E:34 102.0 0.567 E -126.4 139.0 102.0 0.567 0.0 HOH
 2.875
 OE1
 O
GLN H:33 H:34 101.0 0.561 E -109.4 153.4 101.0 0.561 0.0 HOH
 8.051
 NE2
 O
GLN K:33 K:34 97.0 0.539 E -112.8 145.8 97.0 0.539 0.0 EDO
HOH
 6.193
6.338
 OE1
NE2
 O2
O
6sqs 2 P62837 87.67 2e-96 X-RAY
 2020-05-06 GLN B:33 B:34 100.0 0.556 E -107.2 143.9 100.0 0.556 0.0 HOH
 2.525
 OE1
 O
GLN E:33 E:34 103.0 0.572 E -107.5 143.9 103.0 0.572 0.0 HOH
 8.301
 N
 O
5edv 2 P62837 87.67 3e-96 X-RAY
 2016-01-20 GLN C:36 C:34 88.0 0.489 E -116.8 146.9 88.0 0.489 0.0
GLN D:36 D:34 89.0 0.494 E -116.8 146.8 NA NA NA
GLN I:36 I:34 89.0 0.494 E -117.0 146.9 NA NA NA
7jzv 1 A0A386IN42,P61077 87.67 5e-96 EM
 2021-02-17 GLN A:145 A:234 72.0 0.4 E -115.1 155.1 72.0 0.4 0.0
6ttu 6 P62837 87.07 8e-96 EM
 2020-02-12 GLN F:34 D:34 90.0 0.5 E -129.3 116.9 23.0 0.128 0.372 D:Q15843:0.239
A:Q9Y297:0.133
3jvz 1 P62837 86.99 1e-95 X-RAY
 2010-01-12 GLN A:33 A:34 115.0 0.639 E -139.7 131.7 115.0 0.639 0.0
GLN B:33 B:34 94.0 0.522 E -113.0 147.9 NA NA NA
3jw0 1 P62837 86.99 1e-95 X-RAY
 2010-01-12 GLN A:33 A:34 111.0 0.617 E -143.1 136.9 111.0 0.617 0.0
GLN B:33 B:34 109.0 0.606 E -96.9 153.9 NA NA NA
6w7z 1 P62837 86.39 2e-89 X-RAY
 2020-05-20 GLN A:39 A:34 85.0 0.472 E -106.6 144.7 85.0 0.472 0.0 HOH
 3.225
 NE2
 O
5d0k 1 P62837 86.39 7e-89 X-RAY
 2015-12-09 GLN A:39 A:34 102.0 0.567 E -136.4 151.8 102.0 0.567 0.0
GLN C:39 D:34 104.0 0.578 E -136.1 149.4 NA NA NA
GLN E:39 G:34 104.0 0.578 E -137.2 150.6 NA NA NA
GLN G:39 J:34 97.0 0.539 E -136.8 150.4 NA NA NA
5ulh 1 P62837 86.39 7e-89 X-RAY
 2017-06-07 GLN A:39 A:34 110.0 0.611 E -108.6 150.5 110.0 0.611 0.0 GOL
HOH
 7.527
5.078
 O
OE1
 C3
O
5ulk 1 P62837 86.39 7e-89 X-RAY
 2017-06-07 GLN A:39 A:34 90.0 0.5 E -124.1 153.4 49.0 0.272 0.228 B:P0CG47:0.228
6w9d 1 P62837 85.71 2e-88 X-RAY
 2020-05-20 GLN A:34 A:34 85.0 0.472 E -120.6 145.8 85.0 0.472 0.0
GLN D:34 D:34 90.0 0.5 E -116.9 143.6 NA NA NA
GLN G:34 G:34 88.0 0.489 E -118.4 144.3 NA NA NA
5d0m 1 P62837 85.71 3e-88 X-RAY
 2015-12-09 GLN A:39 A:34 111.0 0.617 E -110.0 142.6 111.0 0.617 0.0 HOH
 5.274
 CB
 O
5ulf 1 P62837 85.71 3e-88 X-RAY
 2017-06-07 GLN A:39 A:34 87.0 0.483 E -97.9 141.5 87.0 0.483 0.0 HOH
 3.461
 O
 O
GLN C:39 C:34 90.0 0.5 E -98.1 140.8 NA NA NA
6t7f 2 P61077 85.62 5e-88 X-RAY
 2020-08-05 GLN B:37 B:34 91.0 0.506 E -116.9 151.9 91.0 0.506 0.0 HOH
 3.748
 OE1
 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 GLN A:34 A:34 95.0 0.528 E -101.0 134.3
af-q9y2x8-f1 1 Q9Y2X8 91.84 1e-101 GLN A:34 A:34 97.0 0.539 E -103.1 138.3
af-p62837-f1 1 P62837 89.12 7e-100 GLN A:34 A:34 98.0 0.544 E -102.7 138.7
af-p61077-f1 1 P61077 88.44 2e-99 GLN A:34 A:34 98.0 0.544 E -103.5 137.3