Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr12 56384517 . A C CCDS8900.1:NM_001252036.1:c.367Agt>Cgt_NP_001238965.1:p.123S>R 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: 
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label_comp_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)
2hei 1 P61020 100.0 7e-132 X-RAY
 2006-07-04 SER A:111 A:123 52.0 0.452 -62.5 142.5 52.0 0.452 0.0 HOH
 3.001
 N
 O
SER B:111 B:123 55.0 0.478 -52.9 143.1 21.0 0.183 0.295 A:P61020:0.296
 D1D
HOH
 8.036
2.649
 OG
OG
 S1
O
4q9u 2 P20339 89.35 6e-115 X-RAY
 2014-07-23 SER B:110 B:123 33.0 0.287 -41.6 109.1 33.0 0.287 0.0
SER F:110 F:123 86.0 0.748 -59.9 146.3 86.0 0.748 0.0
1tu3 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 SER A:110 A:123 33.0 0.287 -54.1 136.6 33.0 0.287 0.0 HOH
 3.000
 N
 O
SER B:110 B:123 58.0 0.504 -50.6 146.4 58.0 0.504 0.0 HOH
 3.022
 O
 O
SER C:110 C:123 35.0 0.304 -51.6 141.2 NA NA NA
SER D:110 NA:NA DO NA DO DO DO NA NA NA
SER E:110 E:123 35.0 0.304 -54.1 132.6 NA NA NA
1tu4 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 SER A:110 A:123 45.0 0.391 -70.6 151.9 45.0 0.391 0.0 HOH
 2.761
 N
 O
SER B:110 B:123 52.0 0.452 -37.6 142.0 NA NA NA
SER C:110 C:123 24.0 0.209 -70.3 151.3 NA NA NA
SER D:110 D:123 48.0 0.417 -45.4 134.0 NA NA NA
1n6h 1 P20339 89.35 7e-115 X-RAY
 2002-11-27 SER A:109 A:123 45.0 0.391 -59.2 137.4 45.0 0.391 0.0 HOH
 2.795
 O
 O
1r2q 1 P20339 89.35 7e-115 X-RAY
 2003-12-23 SER A:109 A:123 48.0 0.417 -56.8 138.3 48.0 0.417 0.0 GOL
GOL
HOH
 5.929
5.325
2.861
 N
O
O
 C2
O1
O
1n6o 1 P20339 88.76 4e-114 X-RAY
 2002-11-27 SER A:109 A:123 42.0 0.365 -57.8 139.5 42.0 0.365 0.0 HOH
 2.681
 O
 O
1n6r 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 SER A:109 A:123 48.0 0.417 -58.1 137.8 48.0 0.417 0.0 HOH
 2.797
 OG
 O
1n6p 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 SER A:109 A:123 44.0 0.383 -58.5 135.0 44.0 0.383 0.0 HOH
 2.792
 O
 O
1n6i 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 SER A:109 A:123 47.0 0.409 -57.0 137.3 47.0 0.409 0.0 HOH
 2.739
 O
 O
1n6k 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 SER A:109 A:123 43.0 0.374 -58.6 139.4 43.0 0.374 0.0 HOH
 2.779
 O
 O
1n6l 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 SER A:109 A:123 48.0 0.417 -58.7 139.1 48.0 0.417 0.0 HOH
 2.807
 O
 O
1n6n 1 P20339 88.76 8e-114 X-RAY
 2002-11-27 SER A:109 A:123 46.0 0.4 -57.4 136.4 46.0 0.4 0.0 HOH
 2.831
 O
 O
3mjh 1 P20339 89.29 1e-113 X-RAY
 2010-05-05 SER A:108 A:123 43.0 0.374 -53.2 136.0 43.0 0.374 0.0 HOH
 2.952
 O
 O
SER C:108 C:123 64.0 0.557 -68.9 136.5 NA NA NA
4kyi 2 P51148 92.17 2e-113 X-RAY
 2014-08-13 SER B:112 B:124 47.0 0.409 -67.2 140.8 47.0 0.409 0.0
SER D:112 D:124 43.0 0.374 -70.1 143.6 NA NA NA
SER F:112 F:124 51.0 0.443 -67.8 140.7 NA NA NA
SER H:112 H:124 50.0 0.435 -66.1 129.7 NA NA NA
1huq 1 P35278 92.68 2e-113 X-RAY
 2001-02-07 SER A:106 A:124 47.0 0.409 -55.2 135.9 47.0 0.409 0.0 HOH
 2.645
 O
 O
1z0d 1 P35278 92.12 2e-113 X-RAY
 2005-07-26 SER A:108 A:124 48.0 0.417 -47.5 139.1 48.0 0.417 0.0 HOH
 2.753
 OG
 O
SER B:108 C:124 45.0 0.391 -54.6 140.5 NA NA NA
1z07 1 P35278 92.07 5e-112 X-RAY
 2005-07-26 SER A:108 A:124 41.0 0.357 -40.6 133.1 41.0 0.357 0.0 HOH
 2.794
 OG
 O
7bl1 6 P20339 88.1 2e-111 EM
 2021-03-03 SER F:108 DDD:123 43.0 0.374 -54.8 133.0 43.0 0.374 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 SER A:123 A:123 47.0 0.409 -60.2 136.4
af-p51148-f1 1 P51148 86.12 8e-137 SER A:124 A:124 52.0 0.452 -62.0 137.3
af-p20339-f1 1 P20339 81.86 1e-135 SER A:123 A:123 48.0 0.417 -60.2 135.3