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3DVN

Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin

Functional Information from PROSITE/UniProt
site_idPS00290
Number of Residues7
DetailsIG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YACEVTH
ChainResidueDetails
ATYR194-HIS200
BTYR201-HIS207

site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
YLYS27-ASP52
XLYS27-ASP52

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsSITE: Interacts with activating enzyme
ChainResidueDetails
YARG54
YARG72
VARG54
VARG72

site_idSWS_FT_FI2
Number of Residues2
DetailsSITE: Essential for function
ChainResidueDetails
YHIS68
VHIS68

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
ChainResidueDetails
YSER65
VSER65

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
ChainResidueDetails
YTHR66
VTHR66

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742
ChainResidueDetails
YGLY76
VGLY76

site_idSWS_FT_FI6
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603
ChainResidueDetails
YLYS6
VLYS6

site_idSWS_FT_FI7
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
ChainResidueDetails
YGLY76
VGLY76

site_idSWS_FT_FI8
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144
ChainResidueDetails
YLYS11
YLYS48
VLYS11
VLYS48

site_idSWS_FT_FI9
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860
ChainResidueDetails
YLYS27
VLYS27

site_idSWS_FT_FI10
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127
ChainResidueDetails
YLYS29
VLYS29

site_idSWS_FT_FI11
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577
ChainResidueDetails
YLYS33
VLYS33

site_idSWS_FT_FI12
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106
ChainResidueDetails
YARG63
VARG63

222036

PDB entries from 2024-07-03

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