Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr3 20017598 . C A CCDS2633.1:NM_004162.4:c.375aaC>aaA_NP_004153.2:p.125N>K Homo sapiens RAB5A, member RAS oncogene family (RAB5A), transcript variant 1, mRNA.
pdb_id: 
label_asym_id: 
label_seq_id: 
label_comp_id: 
auth_asym_id: 
auth_seq_id: 
alphafold_id: 
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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)
4q9u 2 P20339 99.42 2e-126 X-RAY
 2014-07-23 ASN B:112 B:125 154.0 0.963 T -69.7 -12.0 154.0 0.963 0.0
ASN F:112 F:125 104.0 0.65 -75.3 -38.8 104.0 0.65 0.0
1tu3 1 P20339 100.0 3e-126 X-RAY
 2004-10-05 ASN A:112 A:125 98.0 0.613 T -108.0 18.8 98.0 0.613 0.0 HOH
 2.752
 O
 O
ASN B:112 B:125 121.0 0.756 T -89.8 -6.1 121.0 0.756 0.0 HOH
 2.838
 O
 O
ASN C:112 C:125 135.0 0.844 T -102.1 46.1 NA NA NA
ASN D:112 NA:NA DO NA DO DO DO NA NA NA
ASN E:112 E:125 114.0 0.713 T -115.6 28.7 NA NA NA
1tu4 1 P20339 100.0 3e-126 X-RAY
 2004-10-05 ASN A:112 A:125 91.0 0.569 T -100.4 11.9 91.0 0.569 0.0 HOH
 2.759
 O
 O
ASN B:112 B:125 133.0 0.831 T -105.6 14.9 NA NA NA
ASN C:112 C:125 87.0 0.544 T -110.1 18.4 NA NA NA
ASN D:112 D:125 136.0 0.85 T -103.5 7.2 NA NA NA
1n6h 1 P20339 100.0 3e-126 X-RAY
 2002-11-27 ASN A:111 A:125 141.0 0.881 T -103.3 9.2 141.0 0.881 0.0 HOH
 2.882
 O
 O
1r2q 1 P20339 100.0 3e-126 X-RAY
 2003-12-23 ASN A:111 A:125 129.0 0.806 T -103.4 11.7 129.0 0.806 0.0 GOL
GOL
HOH
 9.488
4.864
2.340
 N
C
OD1
 O2
O1
O
1n6p 1 P20339 99.41 2e-125 X-RAY
 2002-11-27 ASN A:111 A:125 143.0 0.894 T -100.9 8.5 143.0 0.894 0.0 HOH
 2.968
 O
 O
1n6o 1 P20339 99.41 2e-125 X-RAY
 2002-11-27 ASN A:111 A:125 139.0 0.869 T -100.0 13.2 139.0 0.869 0.0 HOH
 2.786
 O
 O
1n6r 1 P20339 99.41 2e-125 X-RAY
 2002-11-27 ASN A:111 A:125 151.0 0.944 T -103.7 18.1 151.0 0.944 0.0 HOH
 2.777
 ND2
 O
1n6n 1 P20339 99.41 3e-125 X-RAY
 2002-11-27 ASN A:111 A:125 146.0 0.912 T -98.7 10.3 146.0 0.912 0.0 HOH
 2.914
 O
 O
1n6i 1 P20339 99.41 4e-125 X-RAY
 2002-11-27 ASN A:111 A:125 141.0 0.881 T -99.6 11.5 141.0 0.881 0.0 HOH
 2.885
 ND2
 O
1n6k 1 P20339 99.41 4e-125 X-RAY
 2002-11-27 ASN A:111 A:125 141.0 0.881 T -99.3 10.4 141.0 0.881 0.0 HOH
 2.639
 OD1
 O
1n6l 1 P20339 99.41 4e-125 X-RAY
 2002-11-27 ASN A:111 A:125 148.0 0.925 T -103.2 16.4 148.0 0.925 0.0 HOH
 2.950
 O
 O
3mjh 1 P20339 99.4 2e-123 X-RAY
 2010-05-05 ASN A:110 A:125 100.0 0.625 T -82.0 -4.0 100.0 0.625 0.0 HOH
 2.723
 O
 O
ASN C:110 C:125 147.0 0.919 T -106.2 20.1 NA NA NA
7bl1 6 P20339 98.21 2e-121 EM
 2021-03-03 ASN F:110 DDD:125 100.0 0.625 T -80.8 -8.0 100.0 0.625 0.0
2hei 1 P61020 88.14 2e-119 X-RAY
 2006-07-04 SER A:113 A:125 101.0 0.878 T -84.5 -1.9 101.0 0.878 0.0 HOH
 2.578
 OG
 O
SER B:113 B:125 99.0 0.861 T -86.3 -3.9 10.0 0.087 0.774 A:P61020:0.774
 D1D
HOH
 6.285
2.527
 OG
OG
 S1
O
4kyi 2 P51148 93.41 1e-116 X-RAY
 2014-08-13 ASN B:114 B:126 140.0 0.875 T -100.3 33.7 140.0 0.875 0.0
ASN D:114 D:126 136.0 0.85 S -87.1 59.6 NA NA NA
ASN F:114 F:126 143.0 0.894 T -84.1 41.5 NA NA NA
ASN H:114 H:126 138.0 0.863 T -105.5 7.8 NA NA NA
1huq 1 P35278 94.51 4e-116 X-RAY
 2001-02-07 ASN A:108 A:126 149.0 0.931 T -107.4 12.6 149.0 0.931 0.0 HOH
 2.777
 O
 O
1z0d 1 P35278 93.94 7e-116 X-RAY
 2005-07-26 ASN A:110 A:126 137.0 0.856 T -103.6 9.7 137.0 0.856 0.0 HOH
 2.714
 O
 O
ASN B:110 C:126 135.0 0.844 T -96.6 10.8 NA NA NA
1z07 1 P35278 93.9 8e-115 X-RAY
 2005-07-26 ASN A:110 A:126 140.0 0.875 T -102.0 1.9 140.0 0.875 0.0 HOH
 2.675
 ND2
 O

AlphaFold DB

Entity Residue Monomer View
ID Entity Uniprot Identity Evalue Name Label Auth ASA rASA SS φ ψ
af-p20339-f1 1 P20339 100.0 3e-164 ASN A:125 A:125 153.0 0.956 T -104.3 17.6
af-p51148-f1 1 P51148 87.04 2e-140 ASN A:126 A:126 149.0 0.931 T -99.7 13.7
af-p61020-f1 1 P61020 81.86 1e-135 SER A:125 A:125 91.0 0.791 T -93.3 6.2