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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4K7U

Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 101

Chain	Residue
A	MET1
A	GLU16
B	GLU51
C	HOH201

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 102

Chain	Residue
A	GLU18
A	ZN104
C	ASP21
C	EDO104
C	HOH254

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 103

Chain	Residue
A	ASP21
A	ZN104
A	EDO106
A	HOH241
B	GLU18

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZN A 104

Chain	Residue
A	GLU18
A	ZN102
A	ZN103
A	HOH241
B	GLU18
C	GLU18
C	ZN102
C	HOH233
C	HOH254
C	HOH271

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 105

Chain	Residue
A	THR14
A	LYS33
B	HOH248

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 106

Chain	Residue
A	GLU16
A	GLU18
A	ASP21
A	LYS29
A	ZN103
B	GLU18

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 107

Chain	Residue
A	ASP58
A	HOH260
A	HOH280
B	LEU15
B	GLU16
B	LYS29
C	ACT103

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PEG A 108

Chain	Residue
A	PRO37
A	ASP39
A	HOH283
C	ALA46
C	HIS68
C	HOH217
C	HOH258

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 101

Chain	Residue
A	HIS68
B	LYS6
B	HIS68
B	ACT104
B	HOH256

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 102

Chain	Residue
A	HOH244
B	MET1
B	GLU16
B	ZN103
C	GLU51

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 103

Chain	Residue
A	ASP32
A	HOH244
B	ZN102
C	GLU51
C	HOH242

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT B 104

Chain	Residue
A	LYS6
A	THR66
A	HIS68
B	LYS6
B	HIS68
B	ZN101
B	HOH256
B	HOH277

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 105

Chain	Residue
A	LYS63
B	LYS48
B	GLN49
C	GLN31
C	ASP32
C	HOH218

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 101

Chain	Residue
A	GLU51
C	MET1
C	GLU16
C	HOH222

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 102

Chain	Residue
A	ZN104
B	ASP21
C	GLU18
C	ACT103
C	HOH233

site_id	BC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ACT C 103

Chain	Residue
A	EDO107
B	GLU16
B	GLU18
B	ASP21
B	LYS29
B	HOH265
C	GLU18
C	ZN102
C	HOH271

site_id	BC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 104

Chain	Residue
C	HOH270
C	HOH271
A	GLU18
A	ZN102
C	GLU18
C	ASP21
C	LYS29

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

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

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

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

Chain	Residue	Details
A	THR66
B	THR66
C	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
B	LYS6
C	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
A	GLY76
B	GLY76
C	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
A	LYS11
A	LYS48
B	LYS11
B	LYS48
C	LYS11
C	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
A	LYS27
B	LYS27
C	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

218853

PDB entries from 2024-04-24

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