Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr1 202565976 . T A CCDS1427.1:NM_001136504.1:c.1169gAc>gTc_NP_001129976.1:p.390D>V Homo sapiens synaptotagmin 2 (SYT2), 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)
5w5c 6 P21707 86.52 1e-174 X-RAY
 2017-08-23 ASP F:253 F:392 72.0 0.48 H -54.7 -44.4 72.0 0.48 0.0 HOH
 2.661
 OD2
 O
2r83 1 P21579 86.17 5e-174 X-RAY
 2008-02-12 ASP A:255 A:392 5.0 0.033 H -55.9 -37.9 5.0 0.033 0.0 CL
HOH
 7.311
2.425
 N
OD2
 CL
O
ASP B:255 B:392 5.0 0.033 H -56.3 -38.0 5.0 0.033 0.0 CL
HOH
 7.561
5.143
 N
O
 CL
O
5ccg 5 P21707 86.79 6e-174 X-RAY
 2015-08-12 ASP E:252 E:392 53.0 0.353 H -67.0 -40.7 53.0 0.353 0.0
ASP F:252 F:392 70.0 0.467 H -66.7 -40.1 70.0 0.467 0.0
ASP K:252 K:392 63.0 0.42 H -67.1 -40.8 NA NA NA
5cch 5 P21707 86.79 6e-174 X-RAY
 2015-08-12 ASP E:252 E:392 52.0 0.347 H -64.3 -42.5 52.0 0.347 0.0
ASP F:252 F:392 46.0 0.307 H -63.8 -42.3 46.0 0.307 0.0
5cci 5 P21707 86.79 6e-174 X-RAY
 2015-08-12 ASP E:252 E:392 43.0 0.287 H -74.0 -36.2 43.0 0.287 0.0
ASP F:252 F:392 53.0 0.353 H -75.1 -36.5 53.0 0.353 0.0
6mti 2 P21707 86.79 6e-174 EM
 2019-04-24 ASP B:252 2:673 44.0 0.293 H -74.0 -36.2 44.0 0.293 0.0
ASP C:252 3:673 43.0 0.287 H -73.9 -36.3 43.0 0.287 0.0
ASP D:252 4:673 43.0 0.287 H -73.9 -36.3 43.0 0.287 0.0
ASP E:252 5:673 44.0 0.293 H -73.9 -36.2 44.0 0.293 0.0
5kj7 5 P21707 87.36 6e-174 X-RAY
 2016-10-19 ASP E:252 E:392 53.0 0.353 H -68.9 -39.3 53.0 0.353 0.0
ASP F:252 F:392 70.0 0.467 H -67.4 -41.3 NA NA NA
ASP K:252 K:392 60.0 0.4 H -69.5 -39.8 NA NA NA
5kj8 5 P21707 87.36 6e-174 X-RAY
 2016-10-19 ASP E:252 E:392 54.0 0.36 H -67.1 -41.4 54.0 0.36 0.0
ASP F:252 F:392 65.0 0.433 H -67.2 -40.3 NA NA NA
ASP K:252 K:392 62.0 0.413 H -67.6 -41.1 NA NA NA
6tz3 1 P21579 84.71 1e-84 X-RAY
 2020-05-13 ASP A:128 A:393 41.0 0.273 H -62.9 -42.2 41.0 0.273 0.0 HOH
 2.461
 OD1
 O
2yoa 1 P21707 87.42 2e-84 X-RAY
 2013-03-20 ASP A:123 A:392 48.0 0.32 H -60.9 -44.1 48.0 0.32 0.0 HOH
 2.764
 OD2
 O
ASP B:123 B:392 63.0 0.42 H -62.9 -39.6 NA NA NA
5t0s 1 P46096 87.42 2e-84 X-RAY
 2017-06-14 ASP A:122 A:392 42.0 0.28 H -67.6 -37.9 42.0 0.28 0.0 HOH
 2.520
 OD1
 O
2lha 1 P21579 87.42 3e-84 NMR
 2012-05-02 ASP A:123 A:392 77.0 0.513 H -139.5 -53.1 77.0 0.513 0.0
5w5d 6 P21707 87.42 3e-84 X-RAY
 2017-08-23 ASP F:123 F:392 66.0 0.44 H -57.6 -44.7 66.0 0.44 0.0 HOH
 2.773
 OD2
 O
6u4u 1 P21579 84.71 4e-84 X-RAY
 2020-05-13 ASP A:128 A:393 73.0 0.487 H -62.6 -42.5 73.0 0.487 0.0 SO4
HOH
 8.370
2.395
 OD2
OD1
 O1
O
1tjm 1 P21707 84.81 4e-84 X-RAY
 2004-09-28 ASP A:130 A:392 55.0 0.367 H -62.8 -41.3 55.0 0.367 0.0 HOH
 2.095
 OD2
 H2
1tjx 1 P21707 84.81 4e-84 X-RAY
 2004-11-23 ASP A:130 A:392 56.0 0.373 H -62.7 -41.3 56.0 0.373 0.0 HOH
 2.061
 OD2
 H2
1uov 1 P21707 84.81 4e-84 X-RAY
 2004-09-09 ASP A:130 A:392 56.0 0.373 H -63.0 -42.8 56.0 0.373 0.0 HOH
 2.530
 OD2
 O
1uow 1 P21707 84.81 4e-84 X-RAY
 2004-09-16 ASP A:130 A:392 56.0 0.373 H -62.9 -41.1 56.0 0.373 0.0 HOH
 2.677
 OD2
 O
6u4w 1 P21579 84.08 7e-84 X-RAY
 2020-05-13 ASP A:128 A:393 74.0 0.493 H -62.9 -44.1 74.0 0.493 0.0 HOH
 2.519
 OD2
 O
2n1t 5 P21579 85.81 7e-84 NMR
 2015-06-03 ASP E:130 E:392 21.0 0.14 H -62.2 -40.6 21.0 0.14 0.0
4v11 1 P21579 87.33 1e-83 X-RAY
 2015-02-25 ASP A:121 A:393 63.0 0.42 H -63.7 -39.8 63.0 0.42 0.0 HOH
 2.651
 OD2
 O
5vff 1 P46096 86.75 2e-83 X-RAY
 2018-04-11 ASP A:122 A:392 49.0 0.327 H -64.7 -38.7 49.0 0.327 0.0 HOH
 2.696
 OD1
 O
5vfg 1 P46096 86.75 2e-83 X-RAY
 2018-04-11 ASP A:122 A:392 54.0 0.36 H -65.8 -32.4 54.0 0.36 0.0 HOH
 2.426
 OD1
 O
6u41 1 P21579 84.08 2e-83 X-RAY
 2020-05-13 ASP A:128 A:393 58.0 0.387 H -62.1 -40.9 58.0 0.387 0.0 HOH
 2.543
 OD2
 O
5ccj 1 P21707 84.11 8e-80 X-RAY
 2015-08-12 ASP A:123 A:392 46.0 0.307 H -70.7 -30.6 46.0 0.307 0.0 GOL
HOH
 8.691
2.668
 O
OD1
 C1
O
ASP B:123 B:392 79.0 0.527 H -63.2 -39.2 NA NA NA
ASP C:123 C:392 46.0 0.307 H -72.3 -29.0 NA NA NA
ASP D:123 D:392 78.0 0.52 H -62.9 -41.1 NA NA NA

AlphaFold DB

Entity Residue Monomer View
ID Entity Uniprot Identity Evalue Name Label Auth ASA rASA SS φ ψ
af-q8n9i0-f1 1 Q8N9I0 100.0 0.0 ASP A:390 A:390 51.0 0.34 H -62.2 -39.7