5EMZ

Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue SO4 B 101

Chain	Residue
A	ARG42
A	GLN49
A	ARG72
B	ARG42
B	GLN49
B	ARG72
B	HOH246

---

site_id	AC2
Number of Residues	6
Details	binding site for residue SO4 D 101

Chain	Residue
C	ARG72
D	ARG42
D	GLN49
D	ARG72
C	ARG42
C	GLN49

---

site_id	AC3
Number of Residues	5
Details	binding site for residue SO4 E 101

Chain	Residue
E	ARG42
E	GLN49
E	HOH205
F	ARG42
F	GLN49

---

site_id	AC4
Number of Residues	2
Details	binding site for residue SO4 E 102

Chain	Residue
E	HOH208
E	HOH209

---

site_id	AC5
Number of Residues	21
Details	binding site for Di-peptide LYS D 48 and GLY C 76

Chain	Residue
C	ILE44
C	PHE45
C	ALA46
C	GLY47
C	GLN49
C	LEU50
C	LEU71
C	LEU71
C	LEU73
C	ARG74
C	GLY75
D	ILE44
D	TRP45
D	ALA46
D	ALA46
D	GLY47
D	GLN49
D	LEU50
D	LEU71
D	HOH212
D	HOH226

---

site_id	AC6
Number of Residues	24
Details	binding site for Di-peptide LYS F 48 and GLY E 76

Chain	Residue
A	LEU71
B	ALA46
E	ILE44
E	PHE45
E	ALA46
E	GLY47
E	GLN49
E	LEU50
E	LEU71
E	LEU73
E	ARG74
E	GLY75
E	HOH203
E	HOH207
E	HOH212
E	HOH227
F	ILE44
F	TRP45
F	ALA46
F	GLY47
F	GLN49
F	LEU50
F	LEU71
F	LEU73

---

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGrqleD

Chain	Residue	Details
A	LYS27-ASP52

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	SITE: Interacts with activating enzyme

Chain	Residue	Details
D	ARG54
D	ARG72
F	ARG54
F	ARG72
B	ARG54
B	ARG72

---

site_id	SWS_FT_FI2
Number of Residues	3
Details	SITE: Essential for function

Chain	Residue	Details
D	HIS68
F	HIS68
B	HIS68

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291

Chain	Residue	Details
D	SER65
F	SER65
B	SER65

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457

Chain	Residue	Details
D	THR66
F	THR66
B	THR66

---

site_id	SWS_FT_FI5
Number of Residues	3
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742

Chain	Residue	Details
B	GLY76
D	GLY76
F	GLY76

---

site_id	SWS_FT_FI6
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603

Chain	Residue	Details
B	LYS6
F	LYS6
D	LYS6

---

site_id	SWS_FT_FI7
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
B	GLY76
D	GLY76
F	GLY76

---

site_id	SWS_FT_FI8
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144

Chain	Residue	Details
D	LYS48
F	LYS11
F	LYS48
B	LYS11
B	LYS48
D	LYS11

---

site_id	SWS_FT_FI9
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860

Chain	Residue	Details
B	LYS27
D	LYS27
F	LYS27

---

site_id	SWS_FT_FI10
Number of Residues	3
Details	CROSSLNK: 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

Chain	Residue	Details
B	LYS29
D	LYS29
F	LYS29

---

site_id	SWS_FT_FI11
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577

Chain	Residue	Details
B	LYS33
D	LYS33
F	LYS33

---

site_id	SWS_FT_FI12
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106

Chain	Residue	Details
B	LYS63
D	LYS63
F	LYS63

---