Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr12 56380859 . C A CCDS8900.1:NM_001252036.1:c.115Cgt>Agt_NP_001238965.1:p.39R>S 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:27 A:39 43.0 0.191 H -63.7 -43.6 43.0 0.191 0.0 GDP
HOH
 8.102
2.939
 NH2
O
 O6
O
ARG B:27 B:39 42.0 0.187 H -64.3 -45.7 42.0 0.187 0.0 GDP
HOH
 8.024
2.926
 NH2
O
 O6
O
4q9u 2 P20339 89.35 6e-115 X-RAY
 2014-07-23 ARG B:26 B:39 174.0 0.773 H -67.7 -29.2 174.0 0.773 0.0
ARG F:26 F:39 116.0 0.516 H -77.9 -33.9 116.0 0.516 0.0
1tu3 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 ARG A:26 A:39 65.0 0.289 H -48.1 -67.8 65.0 0.289 0.0 GNP
HOH
 7.279
6.359
 CG
N
 O6
O
ARG B:26 B:39 60.0 0.267 H -57.7 -57.3 60.0 0.267 0.0 GNP
HOH
 7.202
5.115
 CG
O
 O6
O
ARG C:26 C:39 50.0 0.222 H -64.2 -47.9 NA NA NA
ARG D:26 D:39 57.0 0.253 H -42.8 -55.3 NA NA NA
ARG E:26 E:39 52.0 0.231 H -60.4 -51.1 NA NA NA
1tu4 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 ARG A:26 A:39 88.0 0.391 H -59.4 -43.3 88.0 0.391 0.0 GDP
HOH
 7.884
3.001
 CB
NE
 N7
O
ARG B:26 B:39 96.0 0.427 H -57.2 -50.8 NA NA NA
ARG C:26 C:39 90.0 0.4 H -62.8 -42.8 NA NA NA
ARG D:26 D:39 101.0 0.449 H -89.0 -25.4 NA NA NA
1n6h 1 P20339 89.35 7e-115 X-RAY
 2002-11-27 ARG A:25 A:39 52.0 0.231 H -63.7 -44.9 52.0 0.231 0.0 HOH
 2.826
 O
 O
1r2q 1 P20339 89.35 7e-115 X-RAY
 2003-12-23 ARG A:25 A:39 57.0 0.253 H -64.7 -45.3 57.0 0.253 0.0 GNP
HOH
 8.019
2.954
 NH2
NH1
 O6
O
1n6o 1 P20339 88.76 4e-114 X-RAY
 2002-11-27 ARG A:25 A:39 53.0 0.236 H -67.1 -41.8 53.0 0.236 0.0 GNP
HOH
 8.084
2.834
 CB
NH1
 N7
O
1n6r 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 ARG A:25 A:39 62.0 0.276 H -65.4 -44.7 62.0 0.276 0.0 GNP
HOH
 7.995
3.021
 NH1
NH2
 O6
O
1n6p 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 ARG A:25 A:39 58.0 0.258 H -65.4 -46.3 58.0 0.258 0.0 HOH
 2.828
 O
 O
1n6i 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ARG A:25 A:39 52.0 0.231 H -65.3 -45.1 52.0 0.231 0.0 GDP
HOH
 8.003
2.910
 CB
NH1
 N7
O
1n6k 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ARG A:25 A:39 53.0 0.236 H -63.9 -43.4 53.0 0.236 0.0 GDP
HOH
 8.051
2.880
 NH2
NH1
 O6
O
1n6l 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ARG A:25 A:39 53.0 0.236 H -65.2 -42.6 53.0 0.236 0.0 GTP
HOH
 8.046
2.851
 CB
NH1
 N7
O
1n6n 1 P20339 88.76 8e-114 X-RAY
 2002-11-27 ARG A:25 A:39 55.0 0.244 H -65.9 -42.9 55.0 0.244 0.0 GNP
HOH
 8.049
2.650
 CB
O
 N7
O
3mjh 1 P20339 89.29 1e-113 X-RAY
 2010-05-05 ARG A:24 A:39 57.0 0.253 H -62.7 -46.4 57.0 0.253 0.0 GTP
HOH
 7.877
3.284
 CD
NH2
 O6
O
ARG C:24 C:39 47.0 0.209 H -63.8 -47.8 NA NA NA
4kyi 2 P51148 92.17 2e-113 X-RAY
 2014-08-13 ARG B:28 B:40 60.0 0.267 H -70.2 -35.1 60.0 0.267 0.0 GNP
EDO
 8.222
8.076
 NE
N
 O6
C1
ARG D:28 D:40 58.0 0.258 H -64.2 -36.4 NA NA NA
ARG F:28 F:40 73.0 0.324 H -60.1 -37.8 NA NA NA
ARG H:28 H:40 55.0 0.244 H -70.1 -51.8 NA NA NA
1huq 1 P35278 92.68 2e-113 X-RAY
 2001-02-07 ARG A:22 A:40 61.0 0.271 H -63.8 -45.0 61.0 0.271 0.0 GNP
HOH
 7.995
3.041
 NH2
NH1
 O6
O
1z0d 1 P35278 92.12 2e-113 X-RAY
 2005-07-26 ARG A:24 A:40 62.0 0.276 H -65.8 -51.7 62.0 0.276 0.0 GDP
HOH
 8.064
2.576
 CB
O
 O6
O
ARG B:24 C:40 54.0 0.24 H -63.5 -46.6 NA NA NA
1z07 1 P35278 92.07 5e-112 X-RAY
 2005-07-26 ARG A:24 A:40 61.0 0.271 H -65.4 -44.3 61.0 0.271 0.0 GNP
HOH
 8.142
2.864
 NE
NH1
 O6
O
7bl1 6 P20339 88.1 2e-111 EM
 2021-03-03 ARG F:24 DDD:39 56.0 0.249 H -62.2 -45.9 56.0 0.249 0.0 GTP
 7.967
 CD
 O6

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:39 A:39 50.0 0.222 H -62.5 -43.6
af-p51148-f1 1 P51148 86.12 8e-137 ARG A:40 A:40 52.0 0.231 H -62.2 -43.4
af-p20339-f1 1 P20339 81.86 1e-135 ARG A:39 A:39 49.0 0.218 H -63.2 -44.6