Variant
| Genome | Chromosome | Position | VCF ID | Ref | Alt | mRNA Change | mRNA Info | GRCh37 | chr14 | 90455318 | . | G | A | CCDS9888.1:NM_001008744.1:c.1201Gtt>Att_NP_001008744.1:p.401V>I | Homo sapiens tyrosyl-DNA phosphodiesterase 1 (TDP1), transcript variant 1, mRNA. |
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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) | |
| 1qzq | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2004-05-11 | VAL | A:276 | A:401 | 7.0 | 0.045 | B | -124.0 | 138.2 | 7.0 | 0.045 | 0.0 |
HOH |
3.361 |
O |
O |
||
| VAL | B:276 | B:401 | 7.0 | 0.045 | B | -130.7 | 139.0 | 7.0 | 0.045 | 0.0 |
HOH |
3.126 |
O |
O |
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| 6dhu | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 6.0 | 0.039 | B | -131.9 | 135.6 | 6.0 | 0.039 | 0.0 |
GHM HOH |
6.019 3.004 |
N O |
O1 O |
||
| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -135.2 | 133.7 | NA | NA | NA | |||||||||||||
| 6die | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -134.3 | 136.2 | 7.0 | 0.045 | 0.0 |
GHM HOH |
6.035 3.130 |
N O |
O2 O |
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| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -136.2 | 136.6 | NA | NA | NA | |||||||||||||
| 6dih | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -131.2 | 133.6 | 7.0 | 0.045 | 0.0 |
GJS HOH |
7.179 2.933 |
N O |
C09 O |
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| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -133.7 | 134.7 | NA | NA | NA | |||||||||||||
| 6dim | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 9.0 | 0.058 | B | -130.6 | 134.9 | 9.0 | 0.058 | 0.0 |
GJP HOH |
9.749 2.859 |
N O |
C4 O |
||
| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -137.5 | 139.4 | NA | NA | NA | |||||||||||||
| 6djd | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 6.0 | 0.039 | B | -129.8 | 135.9 | 6.0 | 0.039 | 0.0 |
GJP HOH |
9.686 3.001 |
N O |
C4 O |
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| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -130.4 | 135.1 | NA | NA | NA | |||||||||||||
| 6dje | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 10.0 | 0.065 | B | -131.1 | 136.5 | 10.0 | 0.065 | 0.0 |
GNY HOH |
8.417 3.071 |
O O |
C01 O |
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| VAL | B:254 | B:401 | 6.0 | 0.039 | B | -132.4 | 128.9 | NA | NA | NA | |||||||||||||
| 6djf | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -129.9 | 135.4 | 7.0 | 0.045 | 0.0 |
GNV HOH |
9.250 3.817 |
O C |
O10 O |
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| VAL | B:254 | B:401 | 10.0 | 0.065 | B | -132.3 | 138.8 | NA | NA | NA | |||||||||||||
| 6djg | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 9.0 | 0.058 | B | -128.4 | 129.1 | 9.0 | 0.058 | 0.0 |
GNJ HOH |
8.648 3.464 |
O O |
O10 O |
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| VAL | B:254 | B:401 | 10.0 | 0.065 | B | -132.8 | 133.0 | NA | NA | NA | |||||||||||||
| 6djh | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -129.7 | 135.5 | 7.0 | 0.045 | 0.0 |
GNM HOH |
9.632 3.328 |
O O |
BR9 O |
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| VAL | B:254 | B:401 | 9.0 | 0.058 | B | -128.3 | 137.7 | NA | NA | NA | |||||||||||||
| 6dji | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 8.0 | 0.052 | B | -130.6 | 137.0 | 8.0 | 0.052 | 0.0 |
GOG HOH |
6.219 2.745 |
N O |
O09 O |
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| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -136.7 | 133.6 | NA | NA | NA | |||||||||||||
| 6djj | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-05-29 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -133.9 | 130.5 | 7.0 | 0.045 | 0.0 |
GM7 HOH |
7.032 2.844 |
N O |
C04 O |
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| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -134.8 | 132.3 | NA | NA | NA | |||||||||||||
| 6myz | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-11-06 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -130.8 | 134.1 | 7.0 | 0.045 | 0.0 |
K7D HOH |
8.693 2.724 |
O O |
C13 O |
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| VAL | B:254 | B:401 | 10.0 | 0.065 | B | -132.1 | 134.7 | NA | NA | NA | |||||||||||||
| 6mz0 | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-11-06 | VAL | A:254 | A:401 | 8.0 | 0.052 | B | -132.9 | 131.7 | 8.0 | 0.052 | 0.0 |
K7A HOH |
7.656 3.852 |
N O |
O08 O |
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| VAL | B:254 | B:401 | 10.0 | 0.065 | B | -131.4 | 133.9 | NA | NA | NA | |||||||||||||
| 6n0d | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-11-13 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -132.8 | 125.7 | 7.0 | 0.045 | 0.0 |
K8J HOH |
6.954 2.833 |
N O |
C09 O |
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| VAL | B:254 | B:401 | 6.0 | 0.039 | B | -133.5 | 126.5 | NA | NA | NA | |||||||||||||
| 6n0n | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-11-13 | VAL | A:254 | A:401 | 8.0 | 0.052 | B | -132.2 | 127.4 | 8.0 | 0.052 | 0.0 |
KAY HOH |
7.033 2.842 |
N O |
C01 O |
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| VAL | B:254 | B:401 | 6.0 | 0.039 | B | -133.4 | 126.1 | NA | NA | NA | |||||||||||||
| 6n0o | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-11-13 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -130.4 | 131.5 | 7.0 | 0.045 | 0.0 |
K8G HOH |
6.490 2.687 |
O O |
O09 O |
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| VAL | B:254 | B:401 | 8.0 | 0.052 | B | -126.8 | 133.6 | NA | NA | NA | |||||||||||||
| 6n0r | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-11-13 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -130.3 | 130.3 | 7.0 | 0.045 | 0.0 |
K8D HOH |
6.385 2.591 |
N O |
C01 O |
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| VAL | B:254 | B:401 | 6.0 | 0.039 | B | -132.8 | 132.9 | NA | NA | NA | |||||||||||||
| 6n17 | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-07-03 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -129.9 | 136.1 | 7.0 | 0.045 | 0.0 |
K8Y HOH |
4.114 2.358 |
O O |
O03 O |
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| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -131.6 | 135.2 | NA | NA | NA | |||||||||||||
| 6n19 | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-07-03 | VAL | A:254 | A:401 | 7.0 | 0.045 | B | -134.2 | 133.4 | 7.0 | 0.045 | 0.0 |
K8V HOH |
4.305 2.869 |
O O |
C05 O |
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| VAL | B:254 | B:401 | 7.0 | 0.045 | B | -134.5 | 133.9 | NA | NA | NA | |||||||||||||
| 6w4r | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2021-03-17 | VAL | A:254 | A:401 | 5.0 | 0.032 | B | -130.5 | 129.6 | 5.0 | 0.032 | 0.0 |
MPO SZV HOH |
3.187 7.005 3.061 |
O N O |
C3 C05 O |
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| VAL | B:254 | B:401 | 5.0 | 0.032 | B | -132.5 | 130.5 | NA | NA | NA | |||||||||||||
| 6w7j | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2021-03-24 | VAL | A:254 | A:401 | 6.0 | 0.039 | B | -132.5 | 126.9 | 6.0 | 0.039 | 0.0 |
TGM HOH |
6.901 2.952 |
N O |
O03 O |
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| VAL | B:254 | B:401 | 5.0 | 0.032 | B | -135.2 | 128.3 | NA | NA | NA | |||||||||||||
| 6w7k | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2021-03-24 | VAL | A:254 | A:401 | 6.0 | 0.039 | B | -130.8 | 130.4 | 6.0 | 0.039 | 0.0 |
TG7 HOH |
7.060 2.888 |
N O |
C05 O |
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| VAL | B:254 | B:401 | 6.0 | 0.039 | B | -133.9 | 133.1 | NA | NA | NA | |||||||||||||
| 6w7l | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2021-03-24 | VAL | A:254 | A:401 | 5.0 | 0.032 | B | -131.3 | 128.5 | 5.0 | 0.032 | 0.0 |
TGV HOH |
6.964 3.084 |
N O |
O01 O |
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| VAL | B:254 | B:401 | 6.0 | 0.039 | B | -130.8 | 133.5 | NA | NA | NA | |||||||||||||
| 6mj5 | 1 | Q9NUW8 | 100.0 | 0.0 |
X-RAY |
2019-07-03 | VAL | A:253 | A:401 | 7.0 | 0.045 | B | -128.3 | 135.8 | 7.0 | 0.045 | 0.0 |
JTA HOH |
9.055 3.677 |
O O |
O10 O |
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| VAL | B:253 | B:401 | 10.0 | 0.065 | B | -135.2 | 143.4 | NA | NA | NA | |||||||||||||
| 1jy1 | 1 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2002-02-20 | VAL | A:257 | A:401 | 7.0 | 0.045 | B | -129.1 | 136.1 | 7.0 | 0.045 | 0.0 |
HOH |
3.681 |
O |
O |
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| 1mu7 | 1 | 20127586 | 98.92 | 0.0 |
X-RAY |
2003-01-07 | VAL | A:278 | A:401 | 8.0 | 0.052 | B | -132.8 | 129.0 | 8.0 | 0.052 | 0.0 |
WO4 GOL HOH |
9.400 7.299 5.707 |
N N C |
O2 C1 O |
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| VAL | B:278 | B:401 | 8.0 | 0.052 | B | -131.4 | 134.9 | NA | NA | NA | |||||||||||||
| 1mu9 | 1 | 20127586 | 98.92 | 0.0 |
X-RAY |
2003-01-07 | VAL | A:278 | A:401 | 9.0 | 0.058 | B | -134.9 | 122.8 | 9.0 | 0.058 | 0.0 |
VO4 GOL HOH |
8.212 8.437 5.567 |
N N O |
O4 C1 O |
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| VAL | B:278 | B:401 | 7.0 | 0.045 | B | -130.6 | 131.3 | NA | NA | NA | |||||||||||||
| 1nop | 2 | 20127586 | 98.92 | 0.0 |
X-RAY |
2003-03-11 | VAL | C:278 | A:401 | 7.0 | 0.045 | B | -130.6 | 112.2 | 7.0 | 0.045 | 0.0 |
DG DT DT VO4 HOH |
8.098 5.849 4.489 8.358 5.883 |
O O N N C |
O3' OP2 OP2 O1 O |
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| VAL | D:278 | B:401 | 8.0 | 0.052 | B | -124.0 | 127.4 | NA | NA | NA | |||||||||||||
| 1rff | 2 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2004-03-02 | VAL | C:278 | A:401 | 7.0 | 0.045 | B | -132.2 | 119.1 | 7.0 | 0.045 | 0.0 |
DG DT DT VO4 HOH |
8.238 5.794 4.493 8.536 2.884 |
O O N N N |
O3' OP2 OP2 O1 O |
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| VAL | D:278 | B:401 | 9.0 | 0.058 | B | -127.5 | 126.7 | NA | NA | NA | |||||||||||||
| 1rfi | 2 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2004-03-02 | VAL | C:278 | A:401 | 6.0 | 0.039 | B | -137.1 | 117.5 | 6.0 | 0.039 | 0.0 |
DG DT DC VO4 HOH |
8.205 5.778 4.457 8.434 2.757 |
O O N N N |
O3' OP2 OP2 O1 O |
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| VAL | D:278 | B:401 | 7.0 | 0.045 | B | -126.7 | 126.2 | NA | NA | NA | |||||||||||||
| 1rg1 | 2 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2004-03-02 | VAL | C:278 | A:401 | 6.0 | 0.039 | B | -128.0 | 116.9 | 6.0 | 0.039 | 0.0 |
DG DT DT VO4 OTS HOH |
8.234 5.726 4.452 8.304 8.864 2.789 |
O O N N N O |
O3' OP2 OP2 O1 C5 O |
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| VAL | D:278 | B:401 | 8.0 | 0.052 | B | -122.1 | 123.9 | NA | NA | NA | |||||||||||||
| 1rg2 | 2 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2004-03-02 | VAL | C:278 | A:401 | 6.0 | 0.039 | B | -130.2 | 114.6 | 6.0 | 0.039 | 0.0 |
DG DT DA VO4 OTS OTR HOH |
8.289 5.807 4.513 8.375 8.961 8.961 2.936 |
O O N N N N N |
O3' OP2 OP2 O1 C5 C5 O |
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| VAL | D:278 | B:401 | 9.0 | 0.058 | B | -128.0 | 121.9 | NA | NA | NA | |||||||||||||
| 1rgt | 2 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2004-03-02 | VAL | C:278 | A:401 | 6.0 | 0.039 | B | -131.2 | 117.9 | 6.0 | 0.039 | 0.0 |
DG DT DC VO4 OTS OTR HOH |
8.259 5.761 4.514 8.347 8.851 8.851 2.854 |
O O N N N N N |
O3' OP2 OP2 O1 C5 C5 O |
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| VAL | D:278 | B:401 | 8.0 | 0.052 | B | -125.5 | 125.8 | NA | NA | NA | |||||||||||||
| 1rgu | 2 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2004-03-02 | VAL | C:278 | A:401 | 5.0 | 0.032 | B | -131.8 | 121.2 | 5.0 | 0.032 | 0.0 |
DG DT DG VO4 OTS HOH |
8.177 5.738 4.498 8.313 8.940 2.788 |
O O N N N O |
O3' OP2 OP2 O1 C5 O |
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| VAL | D:278 | B:401 | 7.0 | 0.045 | B | -128.1 | 125.8 | NA | NA | NA | |||||||||||||
| 1rh0 | 2 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2004-03-02 | VAL | C:278 | A:401 | 7.0 | 0.045 | B | -135.3 | 114.1 | 7.0 | 0.045 | 0.0 |
DT DT VO4 OTS HOH |
5.919 4.458 8.351 8.854 2.841 |
O N N N O |
C5' OP2 O1 C5 O |
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| VAL | D:278 | B:401 | 7.0 | 0.045 | B | -132.0 | 122.3 | NA | NA | NA | |||||||||||||
| 5nw9 | 1 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2018-01-10 | VAL | A:278 | A:401 | 6.0 | 0.039 | B | -128.0 | 125.9 | 6.0 | 0.039 | 0.0 |
DA DG DT DA DA DG DT DA HOH |
8.301 5.838 4.487 8.015 8.301 5.838 4.487 8.015 5.948 |
O O C N O O C N C |
O3' OP2 OP2 OP2 O3' OP2 OP2 OP2 O |
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| VAL | B:278 | B:401 | 8.0 | 0.052 | B | -122.1 | 137.2 | NA | NA | NA | |||||||||||||
| 5nwa | 1 | Q9NUW8 | 98.92 | 0.0 |
X-RAY |
2018-01-10 | VAL | A:278 | A:401 | 6.0 | 0.039 | B | -127.8 | 118.3 | 6.0 | 0.039 | 0.0 |
DA DT DT DA |
8.269 5.768 4.413 7.829 |
O O C N |
O3' C5' OP2 OP2 |
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| VAL | C:278 | B:401 | 6.0 | 0.039 | B | -128.1 | 140.5 | NA | NA | NA | |||||||||||||
AlphaFold DB
| Entity | Residue | Monomer | View | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID | Entity | Uniprot | Identity | Evalue | Name | Label | Auth | ASA | rASA | SS | φ | ψ | |
| af-q9nuw8-f1 | 1 | Q9NUW8 | 100.0 | 0.0 | VAL | A:401 | A:401 | 5.0 | 0.032 | B | -125.0 | 121.2 | |