Variant
| Genome | Chromosome | Position | VCF ID | Ref | Alt | mRNA Change | mRNA Info | GRCh37 | chr12 | 56383868 | . | G | A | CCDS8900.1:NM_001252036.1:c.301Gac>Aac_NP_001238965.1:p.101D>N | Homo sapiens RAB5B, member RAS oncogene family (RAB5B), 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) | |
| 2hei | 1 | P61020 | 100.0 | 7e-132 |
X-RAY |
2006-07-04 | ASP | A:89 | A:101 | 13.0 | 0.087 | E | -113.7 | 120.0 | 13.0 | 0.087 | 0.0 |
GDP HOH |
6.932 4.935 |
OD2 OD2 |
O4' O |
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| ASP | B:89 | B:101 | 13.0 | 0.087 | E | -111.1 | 120.7 | 13.0 | 0.087 | 0.0 |
GDP HOH |
6.848 2.664 |
OD2 OD2 |
O4' O |
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| 4q9u | 2 | P20339 | 89.35 | 6e-115 |
X-RAY |
2014-07-23 | ASP | B:88 | B:101 | 9.0 | 0.06 | E | -88.1 | 148.2 | 9.0 | 0.06 | 0.0 | ||||||
| ASP | F:88 | F:101 | 76.0 | 0.507 | -111.6 | 360.0 | 76.0 | 0.507 | 0.0 | ||||||||||||||
| 1tu3 | 1 | P20339 | 89.35 | 7e-115 |
X-RAY |
2004-10-05 | ASP | A:88 | A:101 | 12.0 | 0.08 | E | -96.6 | 113.2 | 12.0 | 0.08 | 0.0 |
GNP HOH |
6.038 5.557 |
OD2 N |
O4' O |
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| ASP | B:88 | B:101 | 13.0 | 0.087 | E | -90.7 | 115.0 | 13.0 | 0.087 | 0.0 |
GNP |
6.310 |
OD2 |
O4' |
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| ASP | C:88 | C:101 | 9.0 | 0.06 | E | -97.4 | 135.0 | NA | NA | NA | |||||||||||||
| ASP | D:88 | D:101 | 13.0 | 0.087 | E | -121.8 | 117.4 | NA | NA | NA | |||||||||||||
| ASP | E:88 | E:101 | 11.0 | 0.073 | E | -98.0 | 105.7 | NA | NA | NA | |||||||||||||
| 1tu4 | 1 | P20339 | 89.35 | 7e-115 |
X-RAY |
2004-10-05 | ASP | A:88 | A:101 | 13.0 | 0.087 | E | -109.1 | 120.5 | 13.0 | 0.087 | 0.0 |
GDP HOH |
6.791 2.566 |
OD2 OD2 |
O4' O |
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| ASP | B:88 | B:101 | 11.0 | 0.073 | E | -111.9 | 121.5 | NA | NA | NA | |||||||||||||
| ASP | C:88 | C:101 | 15.0 | 0.1 | E | -107.8 | 121.1 | NA | NA | NA | |||||||||||||
| ASP | D:88 | D:101 | 9.0 | 0.06 | E | -98.5 | 135.6 | NA | NA | NA | |||||||||||||
| 1n6h | 1 | P20339 | 89.35 | 7e-115 |
X-RAY |
2002-11-27 | ASP | A:87 | A:101 | 13.0 | 0.087 | E | -110.4 | 119.7 | 13.0 | 0.087 | 0.0 |
GNP HOH |
6.742 2.582 |
OD1 OD1 |
O4' O |
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| 1r2q | 1 | P20339 | 89.35 | 7e-115 |
X-RAY |
2003-12-23 | ASP | A:87 | A:101 | 15.0 | 0.1 | E | -108.7 | 119.8 | 15.0 | 0.1 | 0.0 |
GNP GOL GOL GOL HOH |
6.840 8.135 6.373 2.591 2.622 |
OD2 OD2 OD1 OD2 OD2 |
O4' O1 C1 O3 O |
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| 1n6o | 1 | P20339 | 88.76 | 4e-114 |
X-RAY |
2002-11-27 | ASP | A:87 | A:101 | 12.0 | 0.08 | E | -108.9 | 118.3 | 12.0 | 0.08 | 0.0 |
GNP HOH |
6.648 2.536 |
OD1 OD1 |
O4' O |
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| 1n6r | 1 | P20339 | 88.76 | 5e-114 |
X-RAY |
2002-11-27 | ASP | A:87 | A:101 | 14.0 | 0.093 | E | -110.2 | 120.7 | 14.0 | 0.093 | 0.0 |
GNP HOH |
6.728 2.566 |
OD1 OD1 |
O4' O |
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| 1n6p | 1 | P20339 | 88.76 | 5e-114 |
X-RAY |
2002-11-27 | ASP | A:87 | A:101 | 12.0 | 0.08 | E | -109.8 | 119.8 | 12.0 | 0.08 | 0.0 |
GNP HOH |
6.676 2.635 |
OD1 OD1 |
O4' O |
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| 1n6i | 1 | P20339 | 88.76 | 7e-114 |
X-RAY |
2002-11-27 | ASP | A:87 | A:101 | 9.0 | 0.06 | E | -112.5 | 121.7 | 9.0 | 0.06 | 0.0 |
GDP HOH |
6.752 2.579 |
OD1 OD1 |
O4' O |
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| 1n6k | 1 | P20339 | 88.76 | 7e-114 |
X-RAY |
2002-11-27 | ASP | A:87 | A:101 | 10.0 | 0.067 | E | -108.8 | 121.8 | 10.0 | 0.067 | 0.0 |
GDP HOH |
6.776 2.582 |
OD1 OD1 |
O4' O |
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| 1n6l | 1 | P20339 | 88.76 | 7e-114 |
X-RAY |
2002-11-27 | ASP | A:87 | A:101 | 15.0 | 0.1 | E | -111.2 | 121.5 | 15.0 | 0.1 | 0.0 |
GTP HOH |
6.877 2.584 |
OD1 OD1 |
O4' O |
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| 1n6n | 1 | P20339 | 88.76 | 8e-114 |
X-RAY |
2002-11-27 | ASP | A:87 | A:101 | 13.0 | 0.087 | E | -109.3 | 119.7 | 13.0 | 0.087 | 0.0 |
GNP HOH |
6.673 2.590 |
OD1 OD1 |
O4' O |
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| 3mjh | 1 | P20339 | 89.29 | 1e-113 |
X-RAY |
2010-05-05 | ASP | A:86 | A:101 | 15.0 | 0.1 | E | -111.0 | 118.2 | 15.0 | 0.1 | 0.0 |
GTP HOH |
6.790 2.592 |
OD2 OD2 |
O4' O |
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| ASP | C:86 | C:101 | 14.0 | 0.093 | E | -105.7 | 125.1 | NA | NA | NA | |||||||||||||
| 4kyi | 2 | P51148 | 92.17 | 2e-113 |
X-RAY |
2014-08-13 | ASP | B:90 | B:102 | 8.0 | 0.053 | E | -110.6 | 135.1 | 8.0 | 0.053 | 0.0 |
GNP |
6.976 |
OD2 |
O4' |
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| ASP | D:90 | D:102 | 13.0 | 0.087 | E | -93.2 | 135.6 | NA | NA | NA | |||||||||||||
| ASP | F:90 | F:102 | 7.0 | 0.047 | E | -90.2 | 146.5 | NA | NA | NA | |||||||||||||
| ASP | H:90 | H:102 | 13.0 | 0.087 | E | -87.7 | 118.5 | NA | NA | NA | |||||||||||||
| 1huq | 1 | P35278 | 92.68 | 2e-113 |
X-RAY |
2001-02-07 | ASP | A:84 | A:102 | 13.0 | 0.087 | E | -107.3 | 116.3 | 13.0 | 0.087 | 0.0 |
GNP HOH |
6.703 2.698 |
OD1 OD1 |
O4' O |
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| 1z0d | 1 | P35278 | 92.12 | 2e-113 |
X-RAY |
2005-07-26 | ASP | A:86 | A:102 | 13.0 | 0.087 | E | -109.0 | 119.2 | 13.0 | 0.087 | 0.0 |
GDP HOH |
6.669 2.600 |
OD2 OD2 |
O4' O |
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| ASP | B:86 | C:102 | 15.0 | 0.1 | E | -103.9 | 120.9 | NA | NA | NA | |||||||||||||
| 1z07 | 1 | P35278 | 92.07 | 5e-112 |
X-RAY |
2005-07-26 | ASP | A:86 | A:102 | 15.0 | 0.1 | E | -111.3 | 116.5 | 15.0 | 0.1 | 0.0 |
GNP HOH |
6.679 2.710 |
OD1 OD1 |
O4' O |
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| 7bl1 | 6 | P20339 | 88.1 | 2e-111 |
EM |
2021-03-03 | ASP | F:86 | DDD:101 | 14.0 | 0.093 | E | -110.2 | 119.3 | 14.0 | 0.093 | 0.0 |
GTP |
6.723 |
OD2 |
O4' |
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AlphaFold DB
| Entity | Residue | Monomer | View | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID | Entity | Uniprot | Identity | Evalue | Name | Label | Auth | ASA | rASA | SS | φ | ψ | |
| af-p61020-f1 | 1 | P61020 | 100.0 | 6e-164 | ASP | A:101 | A:101 | 11.0 | 0.073 | E | -98.0 | 121.3 | |
| af-p51148-f1 | 1 | P51148 | 86.12 | 8e-137 | ASP | A:102 | A:102 | 12.0 | 0.08 | E | -99.0 | 122.0 | |
| af-p20339-f1 | 1 | P20339 | 81.86 | 1e-135 | ASP | A:101 | A:101 | 11.0 | 0.073 | E | -99.2 | 124.2 | |