Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr7 43988251 . T A CCDS5474.1:NM_015983.3:c.219atT>atA_NP_057067.1:p.73I>I 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 ILE A:78 A:73 13.0 0.074 -153.6 133.5 13.0 0.074 0.0
ILE B:78 B:73 12.0 0.069 -149.1 135.7 12.0 0.069 0.0
3tgd 1 P62837 93.2 6e-104 X-RAY
 2011-08-31 ILE A:78 A:73 13.0 0.074 -148.6 143.8 13.0 0.074 0.0 HOH
 2.662
 O
 O
7bol 1 P62837 93.2 9e-104 X-RAY
 2021-03-24 ILE A:74 A:73 16.0 0.091 -152.5 145.8 16.0 0.091 0.0 HOH
 2.242
 H
 O
1w4u 1 P51669 93.2 9e-104 NMR
 2004-11-10 ILE A:73 A:73 11.0 0.063 -159.2 123.4 11.0 0.063 0.0
4a49 2 P62837 93.2 9e-104 X-RAY
 2012-01-25 ILE B:73 B:73 7.0 0.04 -148.5 146.0 7.0 0.04 0.0 HOH
 2.713
 O
 O
4a4b 3 P62837 93.2 9e-104 X-RAY
 2012-01-25 ILE C:73 C:73 13.0 0.074 -142.3 139.1 13.0 0.074 0.0
4a4c 3 P62837 93.2 9e-104 X-RAY
 2012-01-25 ILE C:73 C:73 13.0 0.074 -143.5 156.4 13.0 0.074 0.0
5d1k 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 ILE A:73 A:73 11.0 0.063 -147.1 143.1 11.0 0.063 0.0 EDO
PEG
OXL
HOH
 8.754
6.991
8.740
2.780
 C
N
C
O
 C1
C2
O3
O
5d1l 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 ILE A:73 A:73 13.0 0.074 -151.4 137.3 12.0 0.069 0.005 B:Q96BH1:0.006
 PEG
OXL
HOH
 6.773
8.740
2.829
 N
C
O
 O1
O3
O
5d1m 1 P62837 93.2 9e-104 X-RAY
 2015-10-28 ILE A:73 A:73 12.0 0.069 -150.9 138.9 12.0 0.069 0.0 OXL
PEG
HOH
 8.274
6.864
2.821
 C
N
O
 O3
C1
O
2clw 1 P62837 93.2 1e-103 X-RAY
 2007-06-12 ILE A:91 A:73 12.0 0.069 -151.4 142.6 12.0 0.069 0.0 HOH
 2.883
 O
 O
2clw 2 P62837 93.2 1e-103 X-RAY
 2007-06-12 ILE B:91 B:73 12.0 0.069 -154.4 144.0 NA NA NA
ILE C:91 C:73 10.0 0.057 -146.4 145.2 NA NA NA
ILE D:91 D:73 13.0 0.074 -150.4 145.3 NA NA NA
3eb6 2 P62840 93.2 1e-103 X-RAY
 2008-09-09 ILE B:75 B:73 14.0 0.08 -160.7 143.5 14.0 0.08 0.0
6m2c 1 P62837 93.2 1e-103 X-RAY
 2021-04-07 ILE A:75 A:73 6.0 0.034 -154.4 143.1 6.0 0.034 0.0
ILE B:75 B:73 0.0 0.0 -152.5 140.7 NA NA NA
ILE C:75 C:73 6.0 0.034 -153.5 141.9 NA NA NA
ILE D:75 D:73 10.0 0.057 -152.3 144.9 NA NA NA
2esk 1 P62837 93.2 1e-103 X-RAY
 2005-12-06 ILE A:75 A:73 14.0 0.08 -151.9 145.3 14.0 0.08 0.0 HOH
 2.547
 O
 O
3l1y 1 P62837 92.52 2e-103 X-RAY
 2010-05-05 ILE A:83 A:73 11.0 0.063 -150.4 142.8 11.0 0.063 0.0 HOH
 2.538
 O
 O
3l1z 1 P61077 91.84 4e-103 X-RAY
 2010-05-05 ILE A:83 A:73 1.0 0.006 -160.4 136.6 1.0 0.006 0.0
2esq 1 P62837 92.52 5e-103 X-RAY
 2005-12-06 ILE A:75 A:73 12.0 0.069 -152.5 144.0 12.0 0.069 0.0 HOH
 2.652
 O
 O
2eso 1 P62837 92.52 6e-103 X-RAY
 2005-12-06 ILE A:75 A:73 12.0 0.069 -153.2 144.1 12.0 0.069 0.0 HOH
 2.670
 O
 O
2esp 1 P62837 92.52 6e-103 X-RAY
 2005-12-06 ILE A:75 A:73 14.0 0.08 -149.0 146.2 14.0 0.08 0.0 HOH
 2.593
 O
 O
5egg 1 P61077 91.84 8e-103 X-RAY
 2016-11-02 ILE A:82 A:73 13.0 0.074 -150.1 144.8 13.0 0.074 0.0 HOH
 2.578
 O
 O
3a33 1 P62837 92.52 1e-102 X-RAY
 2009-11-24 ILE A:76 A:73 11.0 0.063 -143.2 137.0 11.0 0.063 0.0 HOH
 2.686
 O
 O
1x23 1 P61077 91.84 1e-102 X-RAY
 2005-05-03 ILE A:81 A:73 11.0 0.063 -145.8 136.1 11.0 0.063 0.0 HOH
 2.630
 O
 O
ILE B:81 B:73 15.0 0.086 -151.7 142.0 NA NA NA
ILE C:81 C:73 12.0 0.069 -154.4 140.5 NA NA NA
ILE D:81 D:73 13.0 0.074 -148.0 136.4 NA NA NA
4ldt 3 P62837 92.52 2e-102 X-RAY
 2013-08-14 ILE C:74 C:73 5.0 0.029 -147.6 141.3 5.0 0.029 0.0 HOH
 2.778
 O
 O
4wz3 1 P62837 92.52 2e-102 X-RAY
 2015-01-07 ILE A:74 A:73 7.0 0.04 -143.9 144.7 7.0 0.04 0.0 HOH
 2.651
 O
 O
6hpr 3 P62837 92.52 3e-102 X-RAY
 2018-12-12 ILE C:73 C:73 4.0 0.023 -148.2 142.0 4.0 0.023 0.0 HOH
 2.683
 O
 O
4ddg 1 P62837,Q96FW1 92.52 4e-102 X-RAY
 2012-02-22 ILE A:75 A:73 5.0 0.029 -148.9 142.9 5.0 0.029 0.0
ILE B:75 B:73 6.0 0.034 -148.8 143.0 6.0 0.034 0.0
ILE C:75 C:73 5.0 0.029 -148.8 143.0 5.0 0.029 0.0
ILE J:75 J:73 4.0 0.023 -148.9 143.0 NA NA NA
ILE K:75 K:73 6.0 0.034 -148.9 142.9 NA NA NA
ILE L:75 L:73 4.0 0.023 -148.8 143.0 NA NA NA
4ddi 1 P62837,Q96FW1 92.52 4e-102 X-RAY
 2012-02-22 ILE A:75 A:73 4.0 0.023 -152.8 153.1 4.0 0.023 0.0
ILE B:75 B:73 5.0 0.029 -152.7 153.0 5.0 0.029 0.0
ILE C:75 C:73 6.0 0.034 -152.8 153.0 6.0 0.034 0.0
5zbu 1 P62837 92.52 4e-102 X-RAY
 2019-02-27 ILE A:74 C:73 10.0 0.057 -152.3 142.4 10.0 0.057 0.0
ILE B:74 B:73 12.0 0.069 -152.4 144.0 NA NA NA
4s3o 1 P61077 91.78 5e-102 X-RAY
 2015-07-15 ILE A:74 A:73 14.0 0.08 -148.5 144.3 NA NA NA
ILE B:74 D:73 8.0 0.046 -149.3 141.8 8.0 0.046 0.0 HOH
 2.859
 N
 O
3rpg 1 P61077 91.78 5e-102 X-RAY
 2011-08-17 ILE A:75 A:73 4.0 0.023 -146.0 147.5 4.0 0.023 0.0 HOH
 2.456
 O
 O
6cp0 2 P61077 91.16 6e-102 X-RAY
 2018-08-01 ILE B:75 B:73 15.0 0.086 -149.3 130.6 15.0 0.086 0.0
3ugb 1 P61077 91.16 7e-102 X-RAY
 2012-05-16 ILE A:73 A:73 11.0 0.063 -148.2 146.6 11.0 0.063 0.0 GOL
HOH
 9.150
2.593
 CD1
O
 O3
O
4bvu 2 P61077 91.16 7e-102 X-RAY
 2014-01-29 ILE B:73 B:73 13.0 0.074 -150.7 140.6 13.0 0.074 0.0 HOH
 3.640
 CA
 O
1z2u 1 P35129 92.52 8e-102 X-RAY
 2005-03-22 ILE A:76 A:73 7.0 0.04 -151.5 141.0 7.0 0.04 0.0 BU3
HOH
 9.087
2.741
 N
O
 C1
O
5ifr 1 P61077 91.78 8e-102 X-RAY
 2016-05-11 ILE A:77 A:73 8.0 0.046 -146.5 143.3 8.0 0.046 0.0 HOH
 2.662
 O
 O
7lyb 7 P61077 91.78 8e-102 EM
 2021-07-28 ILE J:91 P:73 5.0 0.029 -113.7 131.2 5.0 0.029 0.0
5mnj 1 P62837 91.84 2e-101 X-RAY
 2017-05-31 ILE A:73 A:73 11.0 0.063 -145.8 144.6 11.0 0.063 0.0 HOH
 2.445
 O
 O
ILE E:73 E:73 5.0 0.029 -149.9 148.4 NA NA NA
5vzw 1 P62837 91.84 2e-101 X-RAY
 2017-08-09 ILE A:73 A:73 7.0 0.04 -145.0 148.7 7.0 0.04 0.0 HOH
 2.613
 HG13
 O
ILE E:73 B:73 9.0 0.051 -144.9 148.4 9.0 0.051 0.0
7ahz 2 Q28EY6 91.84 2e-101 X-RAY
 2021-01-20 ILE B:73 BBB:73 8.0 0.046 -143.3 145.1 NA NA NA
ILE E:73 EEE:73 3.0 0.017 -142.2 148.0 NA NA NA
ILE H:73 HHH:73 5.0 0.029 -144.3 145.1 NA NA NA
ILE K:73 KKK:73 8.0 0.046 -142.7 145.2 NA NA NA
7ai0 2 P62837 91.84 2e-101 X-RAY
 2021-01-20 ILE B:73 BBB:73 3.0 0.017 -146.3 143.3 NA NA NA
ILE E:73 EEE:73 7.0 0.04 -147.2 137.0 NA NA NA
7ai1 2 P62837 91.84 2e-101 X-RAY
 2021-01-20 ILE B:73 BBB:73 6.0 0.034 -141.5 150.4 NA NA NA
ILE E:73 EEE:73 9.0 0.051 -143.5 150.4 NA NA NA
3oj4 1 P51668 91.84 2e-101 X-RAY
 2010-12-08 ILE A:79 A:73 10.0 0.057 -146.9 134.2 10.0 0.057 0.0
ILE D:79 D:73 11.0 0.063 -146.7 133.7 NA NA NA
3ptf 1 P51668 91.84 2e-101 X-RAY
 2011-05-11 ILE A:79 A:73 14.0 0.08 -146.5 137.4 14.0 0.08 0.0 HOH
 3.105
 N
 O
ILE B:79 B:73 12.0 0.069 -143.7 144.4 NA NA NA
4r8p 8 Q99496,P61077 91.78 2e-101 X-RAY
 2014-11-05 ILE L:194 L:273 13.0 NA -109.9 135.6 13.0 NA NA DC
DA
 9.361
9.291
 N
N
 N4
N6
ILE N:194 N:273 15.0 0.086 -144.6 132.2 15.0 0.086 0.0 DT
 8.067
 N
 OP1
4v3l 1 P62837 92.47 2e-101 X-RAY
 2015-04-08 ILE A:72 A:73 6.0 0.034 -150.0 141.6 6.0 0.034 0.0 EDO
HOH
 4.249
2.683
 O
O
 O2
O
2yho 2 P51668 91.84 3e-101 X-RAY
 2011-06-29 ILE B:75 B:73 11.0 0.063 -147.1 144.7 11.0 0.063 0.0 ACT
HOH
 5.500
2.705
 N
O
 CH3
O
ILE D:75 D:73 10.0 0.057 -154.2 142.5 NA NA NA
ILE F:75 F:73 13.0 0.074 -153.3 146.3 NA NA NA
ILE H:75 H:73 11.0 0.063 -149.9 147.7 NA NA NA
6d4p 1 P51668 91.84 3e-101 X-RAY
 2019-07-17 ILE A:75 A:73 9.0 0.051 -147.4 141.5 9.0 0.051 0.0 HOH
 2.538
 HA
 O
4qpl 2 P51668 91.84 3e-101 X-RAY
 2014-10-15 ILE B:80 B:73 11.0 0.063 -147.6 145.0 11.0 0.063 0.0 HOH
 2.678
 O
 O
ILE D:80 D:73 9.0 0.051 -148.3 143.9 NA NA NA
2c4p 1 P51668 91.84 3e-101 X-RAY
 2006-11-22 ILE A:91 A:73 12.0 0.069 -147.4 134.6 12.0 0.069 0.0 HOH
 2.924
 O
 O
ILE B:91 B:73 10.0 0.057 -144.3 145.4 NA NA NA
4auq 1 P62837 91.16 8e-101 X-RAY
 2012-08-15 ILE A:73 A:73 11.0 0.063 -150.3 148.1 11.0 0.063 0.0 HOH
 2.608
 O
 O
ILE D:73 D:73 12.0 0.069 -149.2 144.7 12.0 0.069 0.0 HOH
 3.527
 CA
 O
3zni 3 P62837 91.78 1e-100 X-RAY
 2013-07-10 ILE C:72 C:73 9.0 0.051 -148.7 137.8 9.0 0.051 0.0 HOH
 2.727
 O
 O
ILE G:72 G:73 8.0 0.046 -154.7 139.2 NA NA NA
ILE K:72 K:73 8.0 0.046 -151.5 144.9 NA NA NA
ILE O:72 O:73 8.0 0.046 -153.5 138.6 NA NA NA
4v3k 1 P62837 91.78 1e-100 X-RAY
 2015-04-08 ILE A:72 A:73 8.0 0.046 -143.7 146.5 NA NA NA
ILE D:72 D:73 9.0 0.051 -147.4 144.5 9.0 0.051 0.0 HOH
 2.701
 O
 O
6sqo 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 ILE B:72 B:73 8.0 0.046 -150.9 139.3 8.0 0.046 0.0 HOH
 2.646
 O
 O
ILE E:72 E:73 3.0 0.017 -146.7 144.4 3.0 0.017 0.0 HOH
 2.720
 O
 O
6sqr 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 ILE B:72 B:73 8.0 0.046 -145.9 141.0 8.0 0.046 0.0 HOH
 2.708
 O
 O
ILE E:72 E:73 10.0 0.057 -150.6 155.5 10.0 0.057 0.0 HOH
 5.970
 N
 O
ILE H:72 H:73 11.0 0.063 -154.6 142.2 11.0 0.063 0.0 HOH
 2.660
 O
 O
ILE K:72 K:73 6.0 0.034 -151.5 142.4 6.0 0.034 0.0 EDO
HOH
 4.302
2.591
 N
O
 O1
O
6sqs 2 P62837 91.78 1e-100 X-RAY
 2020-05-06 ILE B:72 B:73 6.0 0.034 -148.3 140.3 6.0 0.034 0.0 HOH
 2.669
 O
 O
ILE E:72 E:73 6.0 0.034 -146.7 138.5 6.0 0.034 0.0 HOH
 2.632
 O
 O
5edv 2 P62837 91.78 2e-100 X-RAY
 2016-01-20 ILE C:75 C:73 11.0 0.063 -150.0 142.5 11.0 0.063 0.0
ILE D:75 D:73 11.0 0.063 -150.4 142.5 NA NA NA
ILE I:75 I:73 11.0 0.063 -150.5 142.6 NA NA NA
6ttu 6 P62837 91.16 4e-100 EM
 2020-02-12 ILE F:73 D:73 11.0 0.063 -151.6 169.2 11.0 0.063 0.0
3jvz 1 P62837 91.1 6e-100 X-RAY
 2010-01-12 ILE A:72 A:73 8.0 0.046 -161.9 138.1 8.0 0.046 0.0
ILE B:72 B:73 8.0 0.046 -162.0 137.9 NA NA NA
3jw0 1 P62837 91.1 6e-100 X-RAY
 2010-01-12 ILE A:72 A:73 6.0 0.034 -144.6 140.3 6.0 0.034 0.0
ILE B:72 B:73 9.0 0.051 -126.6 139.5 NA NA NA
5tut 1 P51668 91.16 7e-100 X-RAY
 2017-11-08 ILE A:76 A:73 5.0 0.029 -147.0 148.8 5.0 0.029 0.0
7jzv 1 A0A386IN42,P61077 91.1 8e-100 EM
 2021-02-17 ILE A:184 A:273 1.0 0.006 -117.6 138.9 1.0 0.006 0.0
4ap4 2 P51668 90.48 3e-99 X-RAY
 2012-07-25 ILE B:79 B:73 9.0 0.051 -148.0 146.2 9.0 0.051 0.0 HOH
 2.650
 O
 O
ILE D:79 E:73 6.0 0.034 -145.4 146.6 6.0 0.034 0.0 HOH
 2.696
 N
 O
5fer 2 P51668 90.48 7e-99 X-RAY
 2016-05-18 ILE B:76 B:73 9.0 0.051 -136.4 147.0 9.0 0.051 0.0 HOH
 3.522
 CG1
 O
ILE E:76 E:73 10.0 0.057 -141.1 141.6 10.0 0.057 0.0 HOH
 2.577
 O
 O
6w7z 1 P62837 90.48 1e-93 X-RAY
 2020-05-20 ILE A:78 A:73 8.0 0.046 -152.2 143.2 8.0 0.046 0.0 HOH
 2.615
 O
 O
5d0k 1 P62837 90.48 3e-93 X-RAY
 2015-12-09 ILE A:78 A:73 11.0 0.063 -145.7 139.5 11.0 0.063 0.0
ILE C:78 D:73 10.0 0.057 -146.4 143.0 NA NA NA
ILE E:78 G:73 11.0 0.063 -143.2 144.6 NA NA NA
ILE G:78 J:73 5.0 0.029 -145.9 142.5 NA NA NA
5ulh 1 P62837 90.48 3e-93 X-RAY
 2017-06-07 ILE A:78 A:73 7.0 0.04 -153.7 146.0 7.0 0.04 0.0 SCN
HOH
 4.183
2.600
 N
O
 S
O
5ulk 1 P62837 90.48 3e-93 X-RAY
 2017-06-07 ILE A:78 A:73 5.0 0.029 -150.0 144.5 5.0 0.029 0.0
6w9d 1 P62837 89.8 1e-92 X-RAY
 2020-05-20 ILE A:73 A:73 9.0 0.051 -152.0 138.2 9.0 0.051 0.0
ILE D:73 D:73 6.0 0.034 -152.3 138.7 NA NA NA
ILE G:73 G:73 12.0 0.069 -148.0 142.9 NA NA NA
5d0m 1 P62837 89.8 2e-92 X-RAY
 2015-12-09 ILE A:78 A:73 7.0 0.04 -150.6 145.3 7.0 0.04 0.0 HOH
 2.748
 O
 O
5ulf 1 P62837 89.8 2e-92 X-RAY
 2017-06-07 ILE A:78 A:73 10.0 0.057 -147.9 141.2 10.0 0.057 0.0 GOL
HOH
 8.716
2.831
 N
O
 C3
O
ILE C:78 C:73 11.0 0.063 -148.4 141.4 NA NA NA
6t7f 2 P61077 89.04 6e-92 X-RAY
 2020-08-05 ILE B:76 B:73 12.0 0.069 -145.3 139.6 12.0 0.069 0.0 HOH
 2.702
 N
 O
4ii2 3 P46595 82.31 6e-91 X-RAY
 2013-02-13 ILE C:73 C:73 10.0 0.057 -154.2 135.5 10.0 0.057 0.0 HOH
 2.666
 O
 O
5aie 2 P15731 81.25 1e-89 X-RAY
 2015-04-29 ILE B:84 B:74 11.0 0.063 -127.2 142.6 11.0 0.063 0.0
1qcq 1 P15731 81.25 2e-89 X-RAY
 1999-05-17 ILE A:74 A:74 10.0 0.057 -133.7 147.1 10.0 0.057 0.0
2ayv 1 ? 81.38 3e-89 X-RAY
 2005-09-20 ILE A:93 A:73 11.0 0.063 -161.8 140.9 11.0 0.063 0.0 UNX
HOH
 3.073
2.500
 O
O
 UNK
O
4x57 1 P35131 80.27 3e-89 X-RAY
 2016-01-20 VAL A:104 A:73 12.0 0.077 -137.3 146.2 12.0 0.077 0.0
VAL C:104 C:73 13.0 0.084 -136.5 147.1 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 ILE A:73 A:73 12.0 0.069 -142.1 143.8
af-p62837-f1 1 P62837 93.2 4e-104 ILE A:73 A:73 13.0 0.074 -143.1 144.0
af-p61077-f1 1 P61077 91.84 2e-103 ILE A:73 A:73 13.0 0.074 -143.2 144.6
af-p51668-f1 1 P51668 91.84 1e-101 ILE A:73 A:73 13.0 0.074 -141.3 143.5