Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr12 56383875 . C A CCDS8900.1:NM_001252036.1:c.308aCt>aAt_NP_001238965.1:p.103T>N 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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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 THR A:91 A:103 31.0 0.221 T -90.6 -2.2 31.0 0.221 0.0 GDP
HOH
 7.462
2.696
 CG2
O
 N2
O
THR B:91 B:103 33.0 0.236 T -86.7 -0.4 33.0 0.236 0.0 GDP
HOH
 7.280
3.782
 CG2
OG1
 N2
O
4q9u 2 P20339 89.35 6e-115 X-RAY
 2014-07-23 THR B:90 B:103 43.0 0.307 S -94.0 8.0 43.0 0.307 0.0
THR F:90 NA:NA DO NA DO DO DO NA NA NA
1tu3 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 THR A:90 A:103 39.0 0.279 T -113.0 2.6 39.0 0.279 0.0 GNP
HOH
 7.377
3.264
 CG2
O
 N2
O
THR B:90 B:103 38.0 0.271 T -98.1 23.3 38.0 0.271 0.0 GNP
 7.857
 CG2
 N2
THR C:90 C:103 43.0 0.307 T -86.3 -3.6 NA NA NA
THR D:90 D:103 37.0 0.264 T -85.0 -0.8 NA NA NA
THR E:90 E:103 37.0 0.264 T -107.6 -4.8 NA NA NA
1tu4 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 THR A:90 A:103 36.0 0.257 T -99.7 8.1 36.0 0.257 0.0 GDP
HOH
 7.755
2.721
 CG2
O
 N2
O
THR B:90 B:103 42.0 0.3 T -93.9 4.7 NA NA NA
THR C:90 C:103 34.0 0.243 T -97.0 23.2 NA NA NA
THR D:90 D:103 42.0 0.3 T -89.6 10.6 NA NA NA
1n6h 1 P20339 89.35 7e-115 X-RAY
 2002-11-27 THR A:89 A:103 34.0 0.243 T -94.3 4.4 34.0 0.243 0.0 GNP
HOH
 7.618
2.821
 CG2
OG1
 N2
O
1r2q 1 P20339 89.35 7e-115 X-RAY
 2003-12-23 THR A:89 A:103 39.0 0.279 T -89.1 -0.3 39.0 0.279 0.0 GNP
GOL
GOL
HOH
 7.609
2.813
3.487
2.810
 CG2
O
OG1
OG1
 N2
O1
C3
O
1n6o 1 P20339 88.76 4e-114 X-RAY
 2002-11-27 THR A:89 A:103 35.0 0.25 T -98.3 5.9 35.0 0.25 0.0 GNP
HOH
 7.601
2.819
 CG2
OG1
 N2
O
1n6r 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 THR A:89 A:103 39.0 0.279 T -94.7 2.5 39.0 0.279 0.0 GNP
HOH
 7.591
2.835
 CG2
O
 N2
O
1n6p 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 THR A:89 A:103 36.0 0.257 T -94.3 1.6 36.0 0.257 0.0 GNP
HOH
 7.575
2.810
 CG2
OG1
 N2
O
1n6i 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 THR A:89 A:103 41.0 0.293 T -97.5 3.1 41.0 0.293 0.0 GDP
HOH
 7.574
2.782
 CG2
O
 N2
O
1n6k 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 THR A:89 A:103 40.0 0.286 T -97.0 4.5 40.0 0.286 0.0 GDP
HOH
 7.680
2.862
 CG2
OG1
 N2
O
1n6l 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 THR A:89 A:103 39.0 0.279 T -93.9 5.6 39.0 0.279 0.0 GTP
HOH
 7.628
2.740
 CG2
OG1
 N2
O
1n6n 1 P20339 88.76 8e-114 X-RAY
 2002-11-27 THR A:89 A:103 40.0 0.286 T -98.2 5.3 40.0 0.286 0.0 GNP
HOH
 7.627
2.814
 CG2
OG1
 N2
O
3mjh 1 P20339 89.29 1e-113 X-RAY
 2010-05-05 THR A:88 A:103 42.0 0.3 T -85.9 2.0 42.0 0.3 0.0 GTP
HOH
 7.455
2.595
 CG2
OG1
 N2
O
THR C:88 C:103 36.0 0.257 T -93.6 2.3 NA NA NA
4kyi 2 P51148 92.17 2e-113 X-RAY
 2014-08-13 THR B:92 B:104 41.0 0.293 T -96.5 10.5 41.0 0.293 0.0 GNP
 7.036
 CG2
 N2
THR D:92 D:104 48.0 0.343 T -98.2 16.5 NA NA NA
THR F:92 F:104 53.0 0.379 T -89.4 17.6 NA NA NA
THR H:92 H:104 42.0 0.3 T -88.4 27.8 NA NA NA
1huq 1 P35278 92.68 2e-113 X-RAY
 2001-02-07 THR A:86 A:104 40.0 0.286 T -90.2 -1.0 40.0 0.286 0.0 GNP
HOH
 7.505
2.718
 CG2
O
 N2
O
1z0d 1 P35278 92.12 2e-113 X-RAY
 2005-07-26 THR A:88 A:104 36.0 0.257 T -97.3 11.6 36.0 0.257 0.0 GDP
HOH
 8.098
3.006
 CG2
O
 N2
O
THR B:88 C:104 41.0 0.293 T -90.0 2.7 NA NA NA
1z07 1 P35278 92.07 5e-112 X-RAY
 2005-07-26 THR A:88 A:104 39.0 0.279 T -90.3 -0.3 39.0 0.279 0.0 GNP
HOH
 7.560
2.833
 CG2
O
 N2
O
7bl1 6 P20339 88.1 2e-111 EM
 2021-03-03 THR F:88 DDD:103 40.0 0.286 T -85.9 1.6 40.0 0.286 0.0 GTP
 7.490
 CG2
 N2

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 THR A:103 A:103 26.0 0.186 T -93.6 14.3
af-p51148-f1 1 P51148 86.12 8e-137 THR A:104 A:104 39.0 0.279 T -90.7 3.7
af-p20339-f1 1 P20339 81.86 1e-135 THR A:103 A:103 39.0 0.279 T -92.9 4.6