Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr3 20025202 . A C CCDS2633.1:NM_004162.4:c.535Aaa>Caa_NP_004153.2:p.179K>Q 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: 
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)
4q9u 2 P20339 99.42 2e-126 X-RAY
 2014-07-23 LYS B:166 B:179 161.0 0.805 T -63.7 -8.0 161.0 0.805 0.0
LYS F:166 F:179 172.0 0.86 T -71.1 -11.2 172.0 0.86 0.0
1tu3 1 P20339 100.0 3e-126 X-RAY
 2004-10-05 LYS A:166 A:179 130.0 0.65 H -69.2 -50.2 130.0 0.65 0.0 HOH
 3.095
 CE
 O
LYS B:166 B:179 162.0 0.81 H -69.7 -38.4 162.0 0.81 0.0 HOH
 2.915
 O
 O
LYS C:166 C:179 153.0 0.765 H -86.2 -18.9 NA NA NA
LYS D:166 D:179 161.0 0.805 T -80.0 -9.7 NA NA NA
LYS E:166 E:179 114.0 0.57 H -69.7 -28.5 NA NA NA
1tu4 1 P20339 100.0 3e-126 X-RAY
 2004-10-05 LYS A:166 A:179 175.0 0.875 H -64.1 -27.4 175.0 0.875 0.0 HOH
 3.779
 CB
 O
LYS B:166 B:179 123.0 0.615 H -79.2 -31.5 NA NA NA
LYS C:166 C:179 181.0 0.905 H -61.6 -36.4 NA NA NA
LYS D:166 D:179 159.0 0.795 H -63.1 -34.8 NA NA NA
1n6h 1 P20339 100.0 3e-126 X-RAY
 2002-11-27 LYS A:165 A:179 134.0 0.67 H -63.9 -28.5 134.0 0.67 0.0 HOH
 2.734
 NZ
 O
1r2q 1 P20339 100.0 3e-126 X-RAY
 2003-12-23 LYS A:165 A:179 110.0 0.55 H -67.6 -20.7 110.0 0.55 0.0 HOH
 3.902
 CB
 O
1n6p 1 P20339 99.41 2e-125 X-RAY
 2002-11-27 LYS A:165 A:179 123.0 0.615 H -67.2 -27.4 123.0 0.615 0.0 HOH
 2.855
 O
 O
1n6o 1 P20339 99.41 2e-125 X-RAY
 2002-11-27 LYS A:165 A:179 131.0 0.655 H -64.3 -31.0 131.0 0.655 0.0 HOH
 3.022
 NZ
 O
1n6r 1 P20339 99.41 2e-125 X-RAY
 2002-11-27 LYS A:165 A:179 148.0 0.74 H -63.2 -32.4 148.0 0.74 0.0 HOH
 2.948
 O
 O
1n6n 1 P20339 99.41 3e-125 X-RAY
 2002-11-27 LYS A:165 A:179 123.0 0.615 H -66.6 -28.3 123.0 0.615 0.0 HOH
 2.770
 NZ
 O
1n6i 1 P20339 99.41 4e-125 X-RAY
 2002-11-27 LYS A:165 A:179 106.0 0.53 H -64.7 -28.9 106.0 0.53 0.0 HOH
 2.624
 NZ
 O
1n6k 1 P20339 99.41 4e-125 X-RAY
 2002-11-27 LYS A:165 A:179 130.0 0.65 H -65.5 -27.0 130.0 0.65 0.0 HOH
 2.730
 NZ
 O
1n6l 1 P20339 99.41 4e-125 X-RAY
 2002-11-27 LYS A:165 A:179 117.0 0.585 H -64.7 -27.2 117.0 0.585 0.0 HOH
 2.710
 NZ
 O
3mjh 1 P20339 99.4 2e-123 X-RAY
 2010-05-05 LYS A:164 A:179 153.0 0.765 H -67.6 -41.3 153.0 0.765 0.0 HOH
 3.786
 CG
 O
LYS C:164 C:179 124.0 0.62 H -73.6 -37.1 NA NA NA
7bl1 6 P20339 98.21 2e-121 EM
 2021-03-03 LYS F:164 DDD:179 153.0 0.765 H -70.4 -39.8 153.0 0.765 0.0
2hei 1 P61020 88.14 2e-119 X-RAY
 2006-07-04 LYS A:167 A:179 115.0 0.575 H -65.7 -27.7 115.0 0.575 0.0 HOH
 3.713
 O
 O
LYS B:167 B:179 129.0 0.645 H -66.3 -27.8 129.0 0.645 0.0 HOH
 3.814
 O
 O
4kyi 2 P51148 93.41 1e-116 X-RAY
 2014-08-13 LYS B:168 B:180 134.0 0.67 H -62.5 -37.1 134.0 0.67 0.0
LYS D:168 D:180 146.0 0.73 T -74.2 -27.4 NA NA NA
LYS F:168 F:180 136.0 0.68 H -69.8 -35.1 NA NA NA
LYS H:168 H:180 140.0 0.7 H -71.5 -38.1 NA NA NA
1huq 1 P35278 94.51 4e-116 X-RAY
 2001-02-07 LYS A:162 A:180 110.0 0.55 H -63.4 -33.0 110.0 0.55 0.0 HOH
 2.899
 CE
 O
1z0d 1 P35278 93.94 7e-116 X-RAY
 2005-07-26 LYS A:164 A:180 153.0 0.765 H -71.4 -34.6 153.0 0.765 0.0 HOH
 3.277
 CD
 O
LYS B:164 C:180 155.0 0.775 H -67.7 -33.4 NA NA NA
1z07 1 P35278 93.9 8e-115 X-RAY
 2005-07-26 LYS A:164 A:180 132.0 0.66 H -66.8 -28.7 132.0 0.66 0.0 HOH
 2.810
 NZ
 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 LYS A:179 A:179 141.0 0.705 H -70.0 -29.5
af-p51148-f1 1 P51148 87.04 2e-140 LYS A:180 A:180 139.0 0.695 H -69.7 -29.5
af-p61020-f1 1 P61020 81.86 1e-135 LYS A:179 A:179 122.0 0.61 H -67.3 -29.5