Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr12 56384509 . G A CCDS8900.1:NM_001252036.1:c.359cGa>cAa_NP_001238965.1:p.120R>Q Homo sapiens RAB5B, member RAS oncogene family (RAB5B), 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)
2hei 1 P61020 100.0 7e-132 X-RAY
 2006-07-04 ARG A:108 A:120 165.0 0.733 H -83.4 -27.0 165.0 0.733 0.0 D1D
HOH
 8.843
2.590
 NH2
NH2
 O3
O
ARG B:108 B:120 124.0 NA H -83.0 -32.0 100.0 NA NA A:P61020:NA
 HOH
 5.724
 CD
 O
4q9u 2 P20339 89.35 6e-115 X-RAY
 2014-07-23 ARG B:107 B:120 192.0 0.853 H -75.5 -66.9 192.0 0.853 0.0
ARG F:107 F:120 168.0 0.747 H -74.6 -60.2 168.0 0.747 0.0
1tu3 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 ARG A:107 A:120 162.0 0.72 H -92.3 -34.5 162.0 0.72 0.0 HOH
 4.530
 N
 O
ARG B:107 B:120 186.0 0.827 H -84.3 -40.9 186.0 0.827 0.0 HOH
 4.415
 N
 O
ARG C:107 C:120 163.0 0.724 H -105.4 -26.7 NA NA NA
ARG D:107 NA:NA DO NA DO DO DO NA NA NA
ARG E:107 E:120 166.0 0.738 H -90.7 -28.6 NA NA NA
1tu4 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 ARG A:107 A:120 174.0 0.773 H -75.5 -30.1 174.0 0.773 0.0 HOH
 2.656
 O
 O
ARG B:107 B:120 179.0 0.796 H -83.1 -38.8 NA NA NA
ARG C:107 C:120 193.0 0.858 H -80.9 -38.7 NA NA NA
ARG D:107 D:120 182.0 0.809 H -83.6 -37.1 NA NA NA
1n6h 1 P20339 89.35 7e-115 X-RAY
 2002-11-27 ARG A:106 A:120 164.0 0.729 H -94.5 -28.9 164.0 0.729 0.0 HOH
 3.055
 NH1
 O
1r2q 1 P20339 89.35 7e-115 X-RAY
 2003-12-23 ARG A:106 A:120 171.0 0.76 H -86.2 -34.7 171.0 0.76 0.0 GOL
GOL
HOH
 3.599
8.140
3.628
 O
N
O
 O1
O1
O
1n6o 1 P20339 88.76 4e-114 X-RAY
 2002-11-27 ARG A:106 A:120 180.0 0.8 H -95.4 -28.5 180.0 0.8 0.0 HOH
 2.711
 O
 O
1n6r 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 ARG A:106 A:120 180.0 0.8 H -96.4 -29.8 180.0 0.8 0.0 HOH
 2.977
 NH1
 O
1n6p 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 ARG A:106 A:120 171.0 0.76 H -91.3 -33.6 171.0 0.76 0.0 HOH
 2.875
 NE
 O
1n6i 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ARG A:106 A:120 165.0 0.733 H -94.4 -28.3 165.0 0.733 0.0 HOH
 2.876
 NH1
 O
1n6k 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ARG A:106 A:120 168.0 0.747 H -95.8 -32.0 168.0 0.747 0.0 HOH
 2.880
 NH1
 O
1n6l 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ARG A:106 A:120 181.0 0.804 H -94.9 -30.7 181.0 0.804 0.0 HOH
 3.014
 NH1
 O
1n6n 1 P20339 88.76 8e-114 X-RAY
 2002-11-27 ARG A:106 A:120 184.0 0.818 H -93.9 -31.9 184.0 0.818 0.0 HOH
 2.702
 NH1
 O
3mjh 1 P20339 89.29 1e-113 X-RAY
 2010-05-05 ARG A:105 A:120 146.0 0.649 H -77.2 -36.2 146.0 0.649 0.0 HOH
 4.978
 O
 O
ARG C:105 C:120 128.0 0.569 H -71.6 -19.5 NA NA NA
4kyi 2 P51148 92.17 2e-113 X-RAY
 2014-08-13 ARG B:109 B:121 199.0 0.884 H -71.6 -50.0 199.0 0.884 0.0
ARG D:109 D:121 141.0 0.627 H -107.9 -68.4 NA NA NA
ARG F:109 F:121 138.0 0.613 H -80.1 -37.4 NA NA NA
ARG H:109 H:121 158.0 0.702 H -100.7 -69.1 NA NA NA
1huq 1 P35278 92.68 2e-113 X-RAY
 2001-02-07 ARG A:103 A:121 201.0 0.893 H -103.0 -32.4 201.0 0.893 0.0 HOH
 3.070
 NH1
 O
1z0d 1 P35278 92.12 2e-113 X-RAY
 2005-07-26 ARG A:105 A:121 162.0 0.72 H -87.8 -36.5 162.0 0.72 0.0 HOH
 2.947
 NH2
 O
ARG B:105 C:121 89.0 NA H -97.3 -30.2 NA NA NA
1z07 1 P35278 92.07 5e-112 X-RAY
 2005-07-26 ARG A:105 A:121 82.0 NA H -89.0 -33.5 82.0 NA NA HOH
 3.299
 O
 O
7bl1 6 P20339 88.1 2e-111 EM
 2021-03-03 ARG F:105 DDD:120 145.0 0.644 H -76.9 -37.7 145.0 0.644 0.0

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 ARG A:120 A:120 178.0 0.791 H -80.4 -37.4
af-p51148-f1 1 P51148 86.12 8e-137 ARG A:121 A:121 182.0 0.809 H -82.3 -38.5
af-p20339-f1 1 P20339 81.86 1e-135 ARG A:120 A:120 204.0 0.907 H -88.9 -35.9