5YDK

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue GOL J 101

Chain	Residue
J	MET1
J	GLU16
J	GLU18
J	HOH208
L	TYR145
L	ARG148
L	GLU152

---

site_id	AC2
Number of Residues	7
Details	binding site for residue GOL C 101

Chain	Residue
A	GLU152
C	MET1
C	GLU16
C	HOH207
C	HOH210
A	TYR145
A	ARG148

---

site_id	AC3
Number of Residues	14
Details	binding site for Di-peptide CYS G 190 and CYS F 190

Chain	Residue
C	ARG72
F	ILE186
F	ASN187
F	ASN188
F	PHE189
F	GLU191
G	ILE186
G	ILE186
G	ASN187
G	ASN188
G	PHE189
G	GLU191
J	ARG72
J	ARG72

---

site_id	AC4
Number of Residues	15
Details	binding site for Di-peptide LYS I 63 and GLY H 76

Chain	Residue
G	GLU153
H	MET1
H	GLN62
H	GLU64
H	SER65
H	LEU73
H	GLY75
H	HOH107
I	MET1
I	GLN2
I	GLN62
I	GLU64
I	SER65
I	HOH116
I	HOH119

---

site_id	AC5
Number of Residues	12
Details	binding site for Di-peptide LYS J 63 and GLY K 76

Chain	Residue
J	GLN2
J	GLN62
J	GLU64
J	SER65
J	HOH214
K	MET1
K	GLN62
K	GLU64
K	SER65
K	LEU73
K	ARG74
K	GLY75

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
B	LYS27-ASP52
D	LYS27-ASP52

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	SITE: Interacts with activating enzyme

Chain	Residue	Details
D	ARG54
D	ARG72
J	ARG54
J	ARG72
C	ARG54
C	ARG72
I	ARG54
I	ARG72

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	SITE: Essential for function

Chain	Residue	Details
D	HIS68
J	HIS68
C	HIS68
I	HIS68

---

site_id	SWS_FT_FI3
Number of Residues	4
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
J	SER65
C	SER65
I	SER65

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457

Chain	Residue	Details
D	THR66
J	THR66
C	THR66
I	THR66

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742

Chain	Residue	Details
D	GLY76
J	GLY76
C	GLY76
I	GLY76

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603

Chain	Residue	Details
D	LYS6
J	LYS6
C	LYS6
I	LYS6

---

site_id	SWS_FT_FI7
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
D	GLY76
J	GLY76
C	GLY76
I	GLY76

---

site_id	SWS_FT_FI8
Number of Residues	8
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	LYS11
D	LYS48
J	LYS11
J	LYS48
C	LYS11
C	LYS48
I	LYS11
I	LYS48

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860

Chain	Residue	Details
D	LYS27
J	LYS27
C	LYS27
I	LYS27

---

site_id	SWS_FT_FI10
Number of Residues	4
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
D	LYS29
J	LYS29
C	LYS29
I	LYS29

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577

Chain	Residue	Details
D	LYS33
J	LYS33
C	LYS33
I	LYS33

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106

Chain	Residue	Details
D	LYS63
J	LYS63
C	LYS63
I	LYS63

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