Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr12 56383877 . A C CCDS8900.1:NM_001252036.1:c.310Aat>Cat_NP_001238965.1:p.104N>H 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: 
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 ASN A:92 A:104 59.0 0.369 -135.6 101.3 59.0 0.369 0.0 HOH
 3.379
 CB
 O
ASN B:92 B:104 63.0 0.394 -141.2 104.5 63.0 0.394 0.0 HOH
 4.169
 ND2
 O
4q9u 2 P20339 89.35 6e-115 X-RAY
 2014-07-23 ASN B:91 B:104 78.0 0.487 -141.4 91.1 78.0 0.487 0.0
ASN F:91 F:104 126.0 0.787 360.0 126.0 126.0 0.787 0.0
1tu3 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 ASN A:91 A:104 63.0 0.394 -127.1 99.1 63.0 0.394 0.0 GNP
HOH
 9.961
5.336
 ND2
N
 O4'
O
ASN B:91 B:104 48.0 0.3 -151.5 109.8 48.0 0.3 0.0 HOH
 7.073
 OD1
 O
ASN C:91 C:104 49.0 0.306 -121.3 110.3 NA NA NA
ASN D:91 D:104 50.0 0.312 B -129.6 95.4 NA NA NA
ASN E:91 E:104 56.0 0.35 -122.3 102.5 NA NA NA
1tu4 1 P20339 89.35 7e-115 X-RAY
 2004-10-05 ASN A:91 A:104 71.0 0.444 -135.6 105.6 71.0 0.444 0.0 HOH
 3.502
 OD1
 O
ASN B:91 B:104 68.0 0.425 -138.8 101.7 NA NA NA
ASN C:91 C:104 61.0 0.381 -151.4 97.0 NA NA NA
ASN D:91 D:104 67.0 0.419 -139.1 97.3 NA NA NA
1n6h 1 P20339 89.35 7e-115 X-RAY
 2002-11-27 ASN A:90 A:104 55.0 0.344 -138.3 101.9 55.0 0.344 0.0 HOH
 2.926
 ND2
 O
1r2q 1 P20339 89.35 7e-115 X-RAY
 2003-12-23 ASN A:90 A:104 53.0 0.331 -138.2 101.5 53.0 0.331 0.0 GOL
GOL
GOL
HOH
 5.021
7.617
5.922
2.883
 N
OD1
CB
ND2
 O1
O1
O3
O
1n6o 1 P20339 88.76 4e-114 X-RAY
 2002-11-27 ASN A:90 A:104 48.0 0.3 -136.7 100.1 48.0 0.3 0.0 HOH
 2.961
 ND2
 O
1n6r 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 ASN A:90 A:104 55.0 0.344 -137.6 102.8 55.0 0.344 0.0 HOH
 2.817
 ND2
 O
1n6p 1 P20339 88.76 5e-114 X-RAY
 2002-11-27 ASN A:90 A:104 49.0 0.306 -134.5 102.8 49.0 0.306 0.0 HOH
 2.872
 ND2
 O
1n6i 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ASN A:90 A:104 43.0 0.269 -134.9 99.1 43.0 0.269 0.0 GDP
HOH
 9.977
3.148
 ND2
ND2
 O2B
O
1n6k 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ASN A:90 A:104 46.0 0.287 -134.0 99.7 46.0 0.287 0.0 HOH
 3.273
 ND2
 O
1n6l 1 P20339 88.76 7e-114 X-RAY
 2002-11-27 ASN A:90 A:104 55.0 0.344 -139.7 100.1 55.0 0.344 0.0 HOH
 3.023
 ND2
 O
1n6n 1 P20339 88.76 8e-114 X-RAY
 2002-11-27 ASN A:90 A:104 56.0 0.35 -135.4 101.2 56.0 0.35 0.0 HOH
 2.865
 ND2
 O
3mjh 1 P20339 89.29 1e-113 X-RAY
 2010-05-05 ASN A:89 A:104 58.0 0.362 -134.9 100.0 58.0 0.362 0.0 HOH
 2.921
 OD1
 O
ASN C:89 C:104 53.0 0.331 -133.4 104.6 NA NA NA
4kyi 2 P51148 92.17 2e-113 X-RAY
 2014-08-13 ASN B:93 B:105 64.0 0.4 -149.8 109.2 64.0 0.4 0.0
ASN D:93 D:105 66.0 0.412 -157.1 120.0 NA NA NA
ASN F:93 F:105 60.0 0.375 -158.8 115.0 NA NA NA
ASN H:93 H:105 62.0 0.388 -164.5 112.8 NA NA NA
1huq 1 P35278 92.68 2e-113 X-RAY
 2001-02-07 ASN A:87 A:105 63.0 0.394 -135.1 109.3 63.0 0.394 0.0 HOH
 2.862
 ND2
 O
1z0d 1 P35278 92.12 2e-113 X-RAY
 2005-07-26 ASN A:89 A:105 59.0 0.369 -146.0 100.6 59.0 0.369 0.0 HOH
 2.769
 ND2
 O
ASN B:89 C:105 64.0 0.4 -139.2 108.4 NA NA NA
1z07 1 P35278 92.07 5e-112 X-RAY
 2005-07-26 ASN A:89 A:105 63.0 0.394 -139.9 103.5 63.0 0.394 0.0 HOH
 2.970
 ND2
 O
7bl1 6 P20339 88.1 2e-111 EM
 2021-03-03 ASN F:89 DDD:104 57.0 0.356 -134.2 100.6 57.0 0.356 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 ASN A:104 A:104 57.0 0.356 -147.1 102.8
af-p51148-f1 1 P51148 86.12 8e-137 ASN A:105 A:105 62.0 0.388 -142.7 104.4
af-p20339-f1 1 P20339 81.86 1e-135 ASN A:104 A:104 60.0 0.375 -136.7 103.8