Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr1 230410216 . C A CCDS1582.1:NM_004481.3:c.1466tCg>tAg_NP_004472.1:p.489S>* Homo sapiens polypeptide N-acetylgalactosaminyltransferase 2 (GALNT2), 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)
4d0t 1 Q10471 99.82 0.0 X-RAY
 2014-05-28 SER A:489 A:489 5.0 0.043 -104.6 150.4 NA NA NA
SER B:489 B:489 4.0 0.035 -105.0 147.7 NA NA NA
SER C:489 C:489 4.0 0.035 -104.8 148.1 4.0 0.035 0.0 HOH
 2.972
 OG
 O
SER D:489 D:489 5.0 0.043 -104.1 149.0 NA NA NA
SER E:489 E:489 4.0 0.035 -102.6 149.6 NA NA NA
SER F:489 F:489 8.0 0.07 -101.1 148.8 8.0 0.07 0.0 HOH
 9.504
 O
 O
4d0z 1 Q10471 99.82 0.0 X-RAY
 2014-05-28 SER A:489 A:489 2.0 0.017 -101.4 152.1 NA NA NA
SER B:489 B:489 2.0 0.017 -101.7 147.8 2.0 0.017 0.0 EDO
HOH
 7.498
3.384
 O
CA
 O1
O
SER C:489 C:489 2.0 0.017 -102.2 149.6 NA NA NA
SER D:489 D:489 2.0 0.017 -101.3 149.9 NA NA NA
SER E:489 E:489 3.0 0.026 -102.8 148.4 NA NA NA
SER F:489 F:489 2.0 0.017 -101.3 149.8 NA NA NA
4d11 1 Q10471 99.82 0.0 X-RAY
 2014-05-28 SER A:489 A:489 4.0 0.035 B -110.2 146.3 4.0 0.035 0.0
SER B:489 B:489 4.0 0.035 B -112.2 146.3 4.0 0.035 0.0
SER D:489 D:489 4.0 0.035 B -110.2 146.5 NA NA NA
SER E:489 E:489 4.0 0.035 B -109.2 147.0 NA NA NA
SER F:489 NA:NA DO NA DO DO DO NA NA NA
5ajn 1 Q10471 99.82 0.0 X-RAY
 2015-03-11 SER A:489 A:489 5.0 0.043 -95.6 156.2 5.0 0.043 0.0 HOH
 3.460
 CA
 O
5ajo 1 Q10471 99.82 0.0 X-RAY
 2015-03-11 SER A:489 A:489 2.0 0.017 -95.5 152.2 2.0 0.017 0.0 SO4
HOH
 8.893
3.408
 OG
CA
 O1
O
5ajp 1 Q10471 99.82 0.0 X-RAY
 2015-03-11 SER A:489 A:489 4.0 0.035 -92.1 151.9 4.0 0.035 0.0 SO4
HOH
 9.050
3.426
 OG
CA
 O3
O
5fv9 1 Q10471 99.82 0.0 X-RAY
 2016-03-09 SER A:489 A:489 6.0 0.052 -101.6 156.9 NA NA NA
SER B:489 B:489 5.0 0.043 B -94.2 143.7 NA NA NA
SER C:489 C:489 6.0 0.052 -96.7 149.9 6.0 0.052 0.0 HOH
 3.502
 CA
 O
SER D:489 D:489 6.0 0.052 -95.6 152.0 6.0 0.052 0.0 HOH
 3.792
 CB
 O
SER E:489 E:489 7.0 0.061 -101.6 153.3 NA NA NA
SER F:489 F:489 4.0 0.035 -102.7 150.3 NA NA NA
5ndf 1 Q10471 99.82 0.0 X-RAY
 2017-11-01 SER A:489 A:489 3.0 0.026 -100.3 151.9 NA NA NA
SER B:489 B:489 3.0 0.026 -99.9 151.6 NA NA NA
SER C:489 C:489 4.0 0.035 -100.1 153.0 NA NA NA
SER D:489 D:489 4.0 0.035 -100.5 151.2 NA NA NA
SER E:489 E:489 3.0 0.026 -99.9 151.1 3.0 0.026 0.0 HOH
 3.444
 CB
 O
SER F:489 F:489 4.0 0.035 -99.8 151.5 NA NA NA
4d11 2 Q10471 99.65 0.0 X-RAY
 2014-05-28 SER C:489 C:489 4.0 0.035 B -108.9 146.9 NA NA NA
6nqt 1 Q10471 99.65 0.0 X-RAY
 2020-01-29 SER A:489 A:489 0.0 0.0 -111.5 145.9 0.0 0.0 0.0 HOH
 7.648
 O
 O
SER B:489 B:489 9.0 0.078 B -121.8 146.6 NA NA NA
SER C:489 C:489 1.0 0.009 -114.1 145.3 1.0 0.009 0.0 HOH
 7.802
 O
 O
SER D:489 D:489 8.0 0.07 -113.4 145.6 NA NA NA
SER E:489 E:489 16.0 0.139 B -111.9 144.7 NA NA NA
SER F:489 F:489 4.0 0.035 -114.6 143.2 NA NA NA
2ffu 1 Q10471 100.0 0.0 X-RAY
 2006-01-31 SER A:419 A:489 2.0 0.017 -102.9 162.2 2.0 0.017 0.0 HOH
 2.693
 OG
 O
2ffv 1 Q10471 100.0 0.0 X-RAY
 2006-01-31 SER A:419 A:489 11.0 0.096 -106.0 158.4 11.0 0.096 0.0
SER B:419 B:489 8.0 0.07 B -103.5 148.5 NA NA NA
6e7i 1 Q10471 99.6 0.0 X-RAY
 2020-01-29 SER A:446 A:489 3.0 0.026 -104.5 164.1 3.0 0.026 0.0 HOH
 2.906
 O
 O
6egs 1 Q10471 99.6 0.0 X-RAY
 2018-04-11 SER A:421 A:489 7.0 0.061 -119.7 152.9 7.0 0.061 0.0 HOH
 8.341
 O
 O
SER B:421 B:489 8.0 0.07 -119.4 154.4 NA NA NA

AlphaFold DB

Entity Residue Monomer View
ID Entity Uniprot Identity Evalue Name Label Auth ASA rASA SS φ ψ
af-q10471-f1 1 Q10471 100.0 0.0 SER A:489 A:489 10.0 0.087 -97.9 141.7