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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5NMC

Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	binding site for residue ACT A 101

Chain	Residue
A	GLU16
A	GLU18
A	ASP21
A	LYS29
A	ACT102
A	ZN105
A	ZN106
A	HOH203
B	GLU18

site_id	AC2
Number of Residues	10
Details	binding site for residue ACT A 102

Chain	Residue
A	GLU18
A	ACT101
A	ZN104
A	ZN106
A	HOH203
A	HOH255
C	GLU18
C	ASP21
C	LYS29
C	HOH212

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN A 103

Chain	Residue
A	MET1
A	GLU16
B	GLU51
C	HOH214

site_id	AC4
Number of Residues	5
Details	binding site for residue ZN A 104

Chain	Residue
A	GLU18
A	ACT102
A	ZN106
C	ASP21
C	HOH212

site_id	AC5
Number of Residues	5
Details	binding site for residue ZN A 105

Chain	Residue
A	ASP21
A	ACT101
A	ZN106
A	HOH238
B	GLU18

site_id	AC6
Number of Residues	12
Details	binding site for residue ZN A 106

Chain	Residue
A	GLU18
A	ACT101
A	ACT102
A	ZN104
A	ZN105
A	HOH203
A	HOH238
B	GLU18
B	HOH241
C	GLU18
C	ZN103
C	HOH212

site_id	AC7
Number of Residues	8
Details	binding site for residue ACT B 101

Chain	Residue
A	HOH203
B	GLU16
B	GLU18
B	ASP21
B	LYS29
B	HOH241
C	GLU18
C	ZN103

site_id	AC8
Number of Residues	6
Details	binding site for residue ACT B 102

Chain	Residue
A	LYS6
A	THR66
A	HIS68
B	LYS6
B	HIS68
B	ZN103

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN B 103

Chain	Residue
A	HIS68
B	LYS6
B	HIS68
B	ACT102

site_id	AD1
Number of Residues	4
Details	binding site for residue ZN B 104

Chain	Residue
B	MET1
B	GLU16
B	HOH205
C	GLU51

site_id	AD2
Number of Residues	7
Details	binding site for residue ACT C 101

Chain	Residue
A	ASP39
C	ALA46
C	HIS68
C	ZN104
C	HOH216
C	HOH225
C	HOH226

site_id	AD3
Number of Residues	4
Details	binding site for residue ZN C 102

Chain	Residue
A	GLU51
B	HOH207
C	MET1
C	GLU16

site_id	AD4
Number of Residues	5
Details	binding site for residue ZN C 103

Chain	Residue
A	ZN106
B	ASP21
B	ACT101
B	HOH241
C	GLU18

site_id	AD5
Number of Residues	4
Details	binding site for residue ZN C 104

Chain	Residue
A	ASP39
C	HIS68
C	ACT101
C	HOH226

Functional Information from PROSITE/UniProt

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

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
B	ARG54
B	ARG72
C	ARG54
C	ARG72
A	ARG54
A	ARG72

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

Chain	Residue	Details
B	HIS68
C	HIS68
A	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
B	SER65
C	SER65
A	SER65

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

Chain	Residue	Details
B	THR66
C	THR66
A	THR66

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

Chain	Residue	Details
A	GLY76
B	GLY76
C	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
A	LYS6
C	LYS6
B	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
C	GLY76
A	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
B	LYS48
C	LYS11
C	LYS48
B	LYS11
A	LYS11
A	LYS48

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
C	LYS27
A	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
A	LYS29
B	LYS29
C	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
A	LYS33
B	LYS33
C	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
A	LYS63
B	LYS63
C	LYS63

220472

PDB entries from 2024-05-29

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