Variant
| Genome | Chromosome | Position | VCF ID | Ref | Alt | mRNA Change | mRNA Info | GRCh37 | chr12 | 79747399 | . | G | A | CCDS9017.1:NM_001135805.1:c.928Gat>Aat_NP_001129277.1:p.310D>N | Homo sapiens synaptotagmin 1 (SYT1), transcript variant 1, mRNA. |
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PDB
| Entity | Residue | Monomer | BioUnit | Ligand | View | ||||||||||||||||||
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| 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 | 100.0 | 0.0 |
X-RAY |
2017-08-23 | ASP | F:170 | F:309 | 6.0 | 0.04 | -124.7 | 77.8 | 6.0 | 0.04 | 0.0 |
GOL HOH |
5.569 2.387 |
N OD2 |
O2 O |
|||
| 5ccg | 5 | P21707 | 100.0 | 0.0 |
X-RAY |
2015-08-12 | ASP | E:169 | E:309 | 35.0 | 0.233 | -133.4 | 72.7 | 35.0 | 0.233 | 0.0 |
CA CA |
2.462 6.362 |
OD2 OD2 |
CA CA |
|||
| ASP | F:169 | F:309 | 60.0 | 0.4 | -134.2 | 74.0 | 60.0 | 0.4 | 0.0 |
CA |
2.587 |
OD2 |
CA |
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| ASP | K:169 | K:309 | 23.0 | 0.153 | -135.6 | 72.4 | NA | NA | NA | ||||||||||||||
| 5cch | 5 | P21707 | 100.0 | 0.0 |
X-RAY |
2015-08-12 | ASP | E:169 | E:309 | 18.0 | 0.12 | 51.1 | 41.0 | 18.0 | 0.12 | 0.0 |
CA CA |
3.279 6.600 |
OD2 OD2 |
CA CA |
|||
| ASP | F:169 | F:309 | 46.0 | 0.307 | -137.1 | 89.7 | 46.0 | 0.307 | 0.0 |
CA CA |
2.508 4.431 |
OD2 N |
CA CA |
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| 5cci | 5 | P21707 | 100.0 | 0.0 |
X-RAY |
2015-08-12 | ASP | E:169 | E:309 | 33.0 | 0.22 | -117.9 | 78.0 | 33.0 | 0.22 | 0.0 |
MG |
2.995 |
OD2 |
MG |
|||
| ASP | F:169 | F:309 | 54.0 | 0.36 | -118.6 | 76.4 | 54.0 | 0.36 | 0.0 |
MG |
4.556 |
OD2 |
MG |
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| 6mti | 2 | P21707 | 100.0 | 0.0 |
EM |
2019-04-24 | ASP | B:169 | 2:590 | 33.0 | 0.22 | -117.8 | 77.9 | 33.0 | 0.22 | 0.0 |
MG |
2.994 |
OD2 |
MG |
|||
| ASP | C:169 | 3:590 | 33.0 | 0.22 | -117.9 | 78.1 | 33.0 | 0.22 | 0.0 |
MG |
2.994 |
OD2 |
MG |
||||||||||
| ASP | D:169 | 4:590 | 33.0 | 0.22 | -117.9 | 78.0 | 33.0 | 0.22 | 0.0 |
MG |
2.994 |
OD2 |
MG |
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| ASP | E:169 | 5:590 | 33.0 | 0.22 | -117.9 | 78.0 | 33.0 | 0.22 | 0.0 |
MG |
2.995 |
OD2 |
MG |
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| 2r83 | 1 | P21579 | 99.65 | 0.0 |
X-RAY |
2008-02-12 | ASP | A:172 | A:309 | 27.0 | 0.18 | -128.8 | 68.0 | 27.0 | 0.18 | 0.0 |
HOH |
2.329 |
OD1 |
O |
|||
| ASP | B:172 | B:309 | 27.0 | 0.18 | -128.3 | 66.9 | 27.0 | 0.18 | 0.0 |
HOH |
2.512 |
OD1 |
O |
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| 5kj7 | 5 | P21707 | 100.0 | 0.0 |
X-RAY |
2016-10-19 | ASP | E:169 | E:309 | 34.0 | 0.227 | -132.7 | 74.4 | 34.0 | 0.227 | 0.0 |
CA CA |
2.396 6.402 |
OD2 OD2 |
CA CA |
|||
| ASP | F:169 | F:309 | 60.0 | 0.4 | -137.7 | 76.2 | NA | NA | NA | ||||||||||||||
| ASP | K:169 | K:309 | 21.0 | 0.14 | -135.6 | 75.0 | NA | NA | NA | ||||||||||||||
| 5kj8 | 5 | P21707 | 100.0 | 0.0 |
X-RAY |
2016-10-19 | ASP | E:169 | E:309 | 35.0 | 0.233 | -128.1 | 73.0 | 35.0 | 0.233 | 0.0 |
CA CA |
2.687 6.228 |
OD2 OD2 |
CA CA |
|||
| ASP | F:169 | F:309 | 58.0 | 0.387 | -130.0 | 72.7 | NA | NA | NA | ||||||||||||||
| ASP | K:169 | K:309 | 20.0 | 0.133 | -130.8 | 71.3 | NA | NA | NA | ||||||||||||||
| 2lha | 1 | P21579 | 100.0 | 4e-96 |
NMR |
2012-05-02 | ASP | A:40 | A:309 | 4.0 | 0.027 | -114.9 | 94.3 | 4.0 | 0.027 | 0.0 |
IHP |
3.618 |
HB3 |
O21 |
|||
| 5w5d | 6 | P21707 | 100.0 | 4e-96 |
X-RAY |
2017-08-23 | ASP | F:40 | F:309 | 18.0 | 0.12 | -118.2 | 72.2 | 18.0 | 0.12 | 0.0 |
HOH |
4.165 |
N |
O |
|||
| 5t0s | 1 | P46096 | 100.0 | 2e-95 |
X-RAY |
2017-06-14 | ASP | A:39 | A:309 | 31.0 | 0.207 | -120.5 | 77.4 | 31.0 | 0.207 | 0.0 |
CD HOH |
2.670 3.411 |
OD2 OD2 |
CD O |
|||
| 2yoa | 1 | P21707 | 100.0 | 3e-95 |
X-RAY |
2013-03-20 | ASP | A:40 | A:309 | 4.0 | 0.027 | -122.0 | 74.0 | 4.0 | 0.027 | 0.0 |
CA CA CA SEP CA SCN SCN HOH |
2.353 6.021 9.135 2.800 3.609 7.179 9.551 2.739 |
OD2 OD2 OD2 OD2 CG O CA OD1 |
CA CA CA N CA S C O |
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| ASP | B:40 | B:309 | 4.0 | 0.027 | -124.0 | 72.4 | NA | NA | NA | ||||||||||||||
| 6tz3 | 1 | P21579 | 100.0 | 3e-95 |
X-RAY |
2020-05-13 | ASP | A:45 | A:310 | 32.0 | 0.213 | -118.0 | 78.4 | 32.0 | 0.213 | 0.0 |
SO4 HOH |
9.853 3.263 |
O OD2 |
O2 O |
|||
| 1tjm | 1 | P21707 | 100.0 | 4e-95 |
X-RAY |
2004-09-28 | ASP | A:47 | A:309 | 25.0 | 0.167 | -121.5 | 72.3 | 25.0 | 0.167 | 0.0 |
SR HOH |
2.450 1.690 |
OD1 HB3 |
SR H2 |
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| 1tjx | 1 | P21707 | 100.0 | 4e-95 |
X-RAY |
2004-11-23 | ASP | A:47 | A:309 | 29.0 | 0.193 | -123.5 | 72.8 | 29.0 | 0.193 | 0.0 |
CA CA HOH |
6.091 2.496 2.478 |
OD1 OD1 OD1 |
CA CA H1 |
|||
| 1uov | 1 | P21707 | 100.0 | 4e-95 |
X-RAY |
2004-09-09 | ASP | A:47 | A:309 | 17.0 | 0.113 | -126.1 | 71.5 | 17.0 | 0.113 | 0.0 |
CA CA CA HOH |
5.940 2.350 2.369 3.047 |
OD2 OD2 OD1 OD2 |
CA CA CA O |
|||
| 1uow | 1 | P21707 | 100.0 | 4e-95 |
X-RAY |
2004-09-16 | ASP | A:47 | A:309 | 29.0 | 0.193 | -123.7 | 72.8 | 29.0 | 0.193 | 0.0 |
CA CA HOH |
6.088 2.495 3.002 |
OD1 OD1 OD1 |
CA CA O |
|||
| 4v11 | 1 | P21579 | 100.0 | 2e-94 |
X-RAY |
2015-02-25 | ASP | A:38 | A:310 | 28.0 | 0.187 | -125.0 | 71.5 | 28.0 | 0.187 | 0.0 |
CA CA HOH |
2.370 6.032 2.652 |
OD2 OD2 OD1 |
CA CA O |
|||
| 6u4w | 1 | P21579 | 99.34 | 2e-94 |
X-RAY |
2020-05-13 | ASP | A:45 | A:310 | 13.0 | 0.087 | -128.4 | 76.4 | 13.0 | 0.087 | 0.0 |
SO4 SO4 HOH |
8.730 9.846 2.629 |
HA O OD2 |
O4 O2 O |
|||
| 6u4u | 1 | P21579 | 99.34 | 2e-94 |
X-RAY |
2020-05-13 | ASP | A:45 | A:310 | 15.0 | 0.1 | -130.9 | 76.6 | 15.0 | 0.1 | 0.0 |
SO4 HOH |
8.881 2.553 |
HA OD1 |
O4 O |
|||
| 6u41 | 1 | P21579 | 99.34 | 3e-94 |
X-RAY |
2020-05-13 | ASP | A:45 | A:310 | 16.0 | 0.107 | -126.6 | 76.2 | 16.0 | 0.107 | 0.0 |
SO4 SO4 HOH |
9.836 9.094 2.667 |
O HA OD1 |
O1 O3 O |
|||
| 5vff | 1 | P46096 | 99.34 | 5e-94 |
X-RAY |
2018-04-11 | ASP | A:39 | A:309 | 39.0 | 0.26 | -119.3 | 75.4 | 39.0 | 0.26 | 0.0 |
PB HOH |
2.596 2.943 |
OD2 OD2 |
PB O |
|||
| 5vfg | 1 | P46096 | 99.34 | 5e-94 |
X-RAY |
2018-04-11 | ASP | A:39 | A:309 | 26.0 | 0.173 | -123.0 | 68.4 | 26.0 | 0.173 | 0.0 |
PB HOH |
2.705 2.744 |
OD2 OD2 |
PB O |
|||
| 2n1t | 5 | P21579 | 100.0 | 3e-93 |
NMR |
2015-06-03 | ASP | E:47 | E:309 | 31.0 | 0.207 | -121.0 | 76.0 | 26.0 | 0.173 | 0.034 |
B:P32851:0.033 |
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| 5ccj | 1 | P21707 | 96.69 | 7e-91 |
X-RAY |
2015-08-12 | ASP | A:40 | A:309 | 26.0 | 0.173 | -120.9 | 84.0 | 26.0 | 0.173 | 0.0 |
GOL GOL SO4 HOH |
7.559 9.338 9.884 2.605 |
O N O OD2 |
C1 O1 O1 O |
|||
| ASP | B:40 | B:309 | 16.0 | 0.107 | -127.1 | 77.7 | NA | NA | NA | ||||||||||||||
| ASP | C:40 | C:309 | 20.0 | 0.133 | -131.1 | 77.4 | NA | NA | NA | ||||||||||||||
| ASP | D:40 | D:309 | 26.0 | 0.173 | -124.3 | 81.0 | NA | NA | NA | ||||||||||||||
AlphaFold DB
| Entity | Residue | Monomer | View | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID | Entity | Uniprot | Identity | Evalue | Name | Label | Auth | ASA | rASA | SS | φ | ψ | |
| af-p21579-f1 | 1 | P21579 | 100.0 | 0.0 | ASP | A:310 | A:310 | 21.0 | 0.14 | -105.5 | 65.9 | ||