eF-site ID 3dvg-ABXY PDB Code 3dvg Chain A, B, X, Y click to enlarge Title Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin Classification IMMUNE SYSTEM Compound Human IgG1 fab fragment light chain Source (UBIQ_HUMAN) Sequence A:  TQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAP KLLIYSARSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFA TYYCQQYSSYSSLFTFGQGTKVEIKRTVAAPSVFIFPPSD EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQES VTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLS SPVTKSFNRG B:  EVQLVESGGGLVQPGGSLRLSCAASGFNVKTGLIHWVRQA PGKGLEWVAYITPYYGSTSYADSVKGRFTISADTSKNTAY LQMNSLRAEDTAVYYCAREYYRWYTAIDYWGQGTLVTVSS ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQT YICNVNHKPSNTKVDKKVEPK X:  SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL Y:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG Description Functional site 1) chain Y residue 66 type MOD_RES sequence T description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 source Swiss-Prot : SWS_FT_FI4 2) chain Y residue 54 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 3) chain Y residue 72 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 4) chain Y residue 68 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 5) chain Y residue 65 type MOD_RES sequence S description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 6) chain Y residue 63 type CROSSLNK sequence R description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 source Swiss-Prot : SWS_FT_FI12 7) chain Y residue 29 type CROSSLNK sequence K description 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 source Swiss-Prot : SWS_FT_FI10 8) chain Y residue 76 type MOD_RES sequence G description ADP-ribosylglycine => ECO:0000269|PubMed:28525742 source Swiss-Prot : SWS_FT_FI5 9) chain Y residue 76 type CROSSLNK sequence G description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) source Swiss-Prot : SWS_FT_FI7 10) chain Y residue 11 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 11) chain Y residue 48 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 12) chain Y residue 6 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 source Swiss-Prot : SWS_FT_FI6 13) chain Y residue 33 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 source Swiss-Prot : SWS_FT_FI11 14) chain Y residue 27 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 source Swiss-Prot : SWS_FT_FI9 15) chain X residue 27-52 type prosite sequence KAKIQDKEGIPPDQQRLIFAGKQLED description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD source prosite : PS00299 16) chain Y residue 27-52 type prosite sequence KAKIQDKEGIPPDQQRLIFAGKQLED description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD source prosite : PS00299 17) chain B residue 201-207 type prosite sequence YICNVNH description IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YICNVNH source prosite : PS00290 18) chain A residue 194-200 type prosite sequence YACEVTH description IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YICNVNH source prosite : PS00290

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